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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
History of AFNI updates
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Hi, I'm trying to register a region, originally created with FreeSurfer, to the standard mesh but I got this error message:
SurfToSurf -i_fs /usr/local/freesurfer/subjects/DM/SUMA/std.60.lh.smoothwm.gii -i_fs /usr/local/freesurfer/subjects/DM/SUMA/lh.smoothwm.gii -prefix std.60. -data lh.ffa.niml.dset
oo Warning SUMA_Load_Surface_Object_eng (SUMA_Load_Surface_Object.c:879):
Warnin
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francescastrappini
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AFNI Message Board
Thank you! Is there a reference paper I can read about the HEAT algorithm used for functional data in afni?
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francescastrappini
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AFNI Message Board
Hi all,
I would like to know which model has been implemented for the surface-based spatial smoothing in afni. Heat kernel smoothing and/or diffusion smoothing?
Thank you
Best
Francesca
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francescastrappini
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AFNI Message Board
Hi Rick,
Thank you! Writing the name of the function seems working.
After the the conversion, my second step is:
ConvertDset -i v1s.lh.TS_DM_movie_run1std141.niml.dset -o_NIML -pad_to_node 0 -prefix v2s.lh.TS.DM_movie_run1std141_FULL.niml.dset
It seems working but when I visualize the file on the std 141 surface it crashes while I try to change the threshold of the map.
afni -nim
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francescastrappini
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AFNI Message Board
Hi, I'm trying to convert a functional file from the volume to the surface using the following command:
3dVol2Surf -spec /home/francesca/Desktop/DM/SUMA/std.141.DM_rh.spec -surf_A /home/francesca/Desktop/DM/SUMA/std.141.rh.smoothwm.asc -surf_B /home/francesca/Desktop/DM/SUMA/std.141.rh.pial.asc -sv /home/francesca/Desktop/DM/SUMA/DM_SurfVol+orig.BRIK -grid_parent DM_movie_run2_al+orig.BRI
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francescastrappini
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AFNI Message Board
Thank you so much for the reply!
shalim-ubuntu:/usr/local/freesurfer/subjects/DM/label> 1dcat lh.V2dorsalDM.1D | wc
** FATAL ERROR: Can't read input file 'lh.V2dorsalDM.1D'
** Program compile date = Apr 15 2015
0 0 0
I'm trying to calculate distances between vertices that belong to surface-based regions. So I was trying first to get the coordinate
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francescastrappini
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AFNI Message Board
Thank you!
I's not so clear to me the option -nodes_1D. I tried to load a file that contains the list of nodes of a region and I got this error message:
SurfMeasures -spec /usr/local/freesurfer/subjects/DM/SUMA/DM_lh.spec -sv /usr/local/freesurfer/subjects/DM/SUMA/DM_SurfVol+orig.BRIK -surf_A smoothwm -surf_B pial -func node_volg -func coord_A -func coord_B -nodes_1D 'lh.V2dorsal
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francescastrappini
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AFNI Message Board
Dear Afni experts,
I'm trying to extract voxel-wise timeseries from some surface-based regions with 3dmaskdump. I would like to know the coordinates of the vertices so I used the option -xyz but I got three colomuns of zeros in the output file. Probably I'm doing something wrong...
3dmaskdump -mask lh.DMofa.niml.dset -index -xyz -noijk -o lh_DM_ofa_movie2.txt v2s.lh.TS.DM_movie_ru
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francescastrappini
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AFNI Message Board
Hi Ziad, thank you so much for the help!
I was able to visualize correctly the surface and the regions in SUMA and to extract the timeseries, adding the option -pad_to_node 0 and keeping everything in orig space.
If try to use the standard mesh and I use the option -pad_to_node ld141 my dataset looks ok but the region is distorted, parcelleted and in a wrong position in the surface. I plott
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francescastrappini
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AFNI Message Board
Hi, sorry, I forgot to mention something about the function 3dmaskdump that I used to extract the timeseries from each vertex using a mask.
Looking at the suma_demo, the option -mrange 2 2 prints out only the timeseries associated with the vertexes with value 2. My question is, how do I know into afni/suma which is the value of my region that I used as a mask for extracting the timeseries? With
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francescastrappini
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AFNI Message Board
Hi Ziad, thank you!
You were right, the dataset was wrong. I made a new one and displayed into SUMA. I looked at the timeseries as you suggested and it seems OK. I have a couple of questions:
1. I can display correctly the dataset after 3dVol2Surf, but after performing ConvertDset with the option -pad_to_node ld120 I can't visualize it anymore. SUMA gives me this error: "Error SUM
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francescastrappini
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AFNI Message Board
Thank you!
I tried to run this command line:
3dmaskdump -mask lh.V1dorsalDMfull.1D.dset -index -xyz -o ALL.ts.1D v2s.lh.TS.DM.FULL.niml.dset
In the output I got there are no coordinates and just one value (I suppose the average) for each vertex, so no time series.
I'm sure that there is something important I'm missing but I really can't figure out what...maybe I did not
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francescastrappini
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AFNI Message Board
Hi Ziad,
I ran this command line:
ROI2dataset -prefix lh.V1dorsalDM.1D.dset -of 1D -input lh.V1dorsalDM.1D.roi
I was just trying to follow the procedure in the suma_demo I downloaded, in particular run_ROI2dataset and run_ROI2dump but I probably did not correctly understand some steps.
As you suggested, I tried to add the -padd_to_node option to ROI2dataset and it worked!
Now, I
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francescastrappini
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AFNI Message Board
Hi Afni experts,
I'm having some troubles trying to extract the time series from some surface-based regions I created with freesurfer. I did the following steps:
1. I drew some regions on the individual surfaces with Freesurfer (labels)
2. I created an annot file with mris_label2annot
3. I used FSread_annot to convert the annot file to the .roi file
4. I turned the roi into a datase
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francescastrappini
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AFNI Message Board
Hi,
I'm trying to import some regions drawn on the surface with Freesurfer into SUMA. For each region I have a label and annotation file, should I convert both of them in gifti format to the make the region readable into SUMA?
Thanks!
Best
Francesca
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francescastrappini
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AFNI Message Board
Thank you!
Should I convert just the annot file to gifti format or also the label file?
Best
Francesca
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francescastrappini
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AFNI Message Board
Thank you so much!
I download the new version and I re-ran the analysis but I got the same error:
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank_Alnd_Exp.
removing temporary bricks ...
Done.
foreach hemi ( lh rh )
foreach run ( 01 )
3dVol2Surf -spec /usr/local/freesurfer/subjects/DM/SUMA/DM_lh.spec -sv DM_SurfVol_Alnd_Exp+orig -surf_A smoothwm -surf_
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francescastrappini
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AFNI Message Board
Thank you!
Unfortunately it looks like my afni version is so old that I don't have @update.afni.binaries. Could you please tell me which is the latest version I should download from the website? There are several versions for Linux and it's not clear to me which is the good one. I have Ubuntu 14.04 64.
Sorry, I don't understand exactly what you mean for "prior output&qu
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francescastrappini
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AFNI Message Board
Hi,
I'm trying to run a single subject surface analysis. I ran the script but it ended with this error message:
Done.
foreach hemi ( lh rh )
foreach run ( 01 )
3dVol2Surf -spec /usr/local/freesurfer/subjects/DM/SUMA/DM_lh.spec -sv DM_SurfVol_Alnd_Exp+orig -surf_A smoothwm -surf_B pial -f_index nodes -f_steps 10 -map_func ave -oob_value 0 -grid_parent pb02.DM.r01.volreg+tlrc -out_ni
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francescastrappini
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AFNI Message Board
Hi,
I'm trying to import the ROIs created in the surface with freesurfer using retinotopic data.
I ran this command, and I would like to ask if is it the right procedure. They originally regions were aligned with freesurfer anatomy, I don't know if this registration went lost when I imported the surfaces to SUMA.
FSread_annot -input lh.V3ALG.annot -roi_1D lh.V3ALG.1D.roi -hemi l
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francescastrappini
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AFNI Message Board
Thanks to both of you, it worked!
I'm also tryint to import the ROIs I created in the surface with freesurfer using retinotopic data.
I ran this command, and I would like to ask you if is it the right procedure. They originally were aligned with freesurfer anatomy, I don't know if this registration went lost when I imported the surfaces to SUMA.
FSread_annot -input lh.V3ALG.annot
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francescastrappini
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AFNI Message Board
Hi,
I'm tryint to import some anatomical and functional data from freesurfer to AFNI. I converted the surfaces created with freesurfer with @SUMA_Make_Spec_FS. Now, I would like to align the preprocessed functional runs to the anatomy but unfortunately I did not collect any anatomical scan during the same session of the functional runs. I suppose I can't use @SUMA_AlignToExperiment,
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francescastrappini
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AFNI Message Board