Freesurfer

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16 participants
30084 discussions

Edit pial surface
by Rosalia Dacosta Aguayo 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer's experts, I wonder if there is any chance to correct the pial surface when it does not cover entirely certain regions of GM, such for example, orbital frontal cortex Kind regards, Rosie

2 1

Question about Extracting QDEC Results
by Sonya Gupta 09 Jul '21

09 Jul '21

External Email - Use Caution Hi, Hope you are having a wonderful evening! I was wondering, is there a way to extract results from QDEC as a NIFTI file? If not, in what format can you the extract QDEC results? Thank you! Sincerely, Sonya

2 1

Help segmenting all subjects in a folder
by g.toniol＠libero.it 09 Jul '21

09 Jul '21

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I successfully set up Freesurfer and ran a test on my computer, and I am now attempting to run recon-all on all subjects in a folder ("/home/users/s/saccaro/Groupe_0" in the example script below). I run the analysis on a HPC (SLURM system). I found that, concerning the recon-all command, "If no name is given after --s, the code will be run on ALL subjects in $SUBJECTS_DIR https://secure-web.cisco.com/1cAYZmFGVfas4DCf91-Y9WZa9anAVybKAgr13rFXfcD8Bm… ." but I do not find information on how this could work also for the previous step, mri_convert: is there a way to submit a job to segment all subjects in the folder "Groupe_0", and not just S001 (in the example below)? All folders are structured as follows: /S@@@/scans/struct/@@@@@@.nii . I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. Thank you very much for your time! Best, Giorgio - Script, without SBATCH settings (I join the full version): module load FreeSurfer/6.0.0-centos6_x86_64 source /home/users/s/saccaro/SetUpFreeSurfer.sh FSDIR="/home/users/s/saccaro/Groupe_0" mksubjdris ${FSDIR}/S001; mri_convert -i ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.nii -o ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.mgz recon-all -all -s S001

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fcseed-config
by Nasiriavanaki, Zahra 09 Jul '21

09 Jul '21

Hello Freesurferers, I’m trying to use a functional label (extracted from task functional BOLD data), as a seed for functional connectivity. I tried to use the fcseed-config with -roi , but when I ran the fcseed-sess, I got this error: “If: expression syntax error”. Could you please let me know what the problem is? fcseed-config -roi ${label}.label -fcname ${label}.dat -fsd rest -rlf restruns -mean -cfg ${label}.config -force fcseed-sess -s ${subj} -d ../ -cfg /${label}.config Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

2 1

Can I extract GLM values?
by Thalhammer, Melissa 09 Jul '21

09 Jul '21

External Email - Use Caution Dear FS experts, I have run mris_preproc and mri_glmfit for group analysis as described in the docs. My current project deals with the analysis of cortical thickness of preterm- vs. term-born adults and I want to correlate the difference in cortical thickness between those two groups with gene expression data. Thus, I would need the group difference ROI-wise as values in a spreadsheet/text file to perform correlation lateron. I have used the following code with the --table flag and have used cortical thickness data extracted with aparcstats2table as input. Is there a way to extract the ROI-wise group difference, corrected for the covariates included into my GLM model? Best, Melissa Thalhammer

2 1

mri_glmfit DOSS
by Dr. Cornelius Kronlage 09 Jul '21

09 Jul '21

External Email - Use Caution Dear freesurfers, for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD looks like this: GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ... When I try to run mri_glmfit I get the following error even though I specify DOSS: $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...] gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJk… INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case? Thank you! Best wishes Cornelius

2 1

recon-all soft errors
by Rosalia Dacosta Aguayo 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer team, I am inspecting the different participants I have run recon-all -all and I have found different errors I would like to discuss with you before proceeding as I am new with this software. 1. I have found dura at some regions of the brain. I should use gcut or delete voxels? 2. I have found discontinuity in GM and what I should do with this (attached photo 2) 3. In photo 1, not sure at some regions were to consider wm as it is not clear for me...any suggestion with this one? I think it should be done with cp, right? Kind regards, Rosie

2 1

smoothing volume data extracted using aparcstats2table
by Ryan Bell, Ph.D. 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer Experts, I am wondering whether the extracted ROI volume data acquired when using the command aparcstats2table needs to be smoothed? I performed surface smoothing using surf2surf for cortical thickness data, but cannot find a way to smooth the volume data listed in aparcstats2table. Is it recommended that I do not perform smoothing? Thank You, Ryan ----------------------------------------------------------------------------------------------- Ryan Patrick Bell, Ph.D. Research Analyst, Department of Psychiatry & Behavioral Sciences 905 W. Main St., Suite 24-E Durham, NC 27701 Phone: (919) 681-3495 Email: ryan.bell(a)duke.edu<mailto:ryan.bell@duke.edu> Website: http://secure-web.cisco.com/1fzJIQLKPmbhrC2x32S5RRIKOnZE7eB318ehdee9qx2NWta… Twitter: twitter.com/HARPatDuke<https://secure-web.cisco.com/1K3qzDbdESi5BxKdIeeFsl0dti1McxRsbgZL6xE6fNf4Bc…>

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Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient and corresponding surface map
by Hye Min Shin 09 Jul '21

09 Jul '21

External Email - Use Caution Thank you for the response Bruce. I apologize for the confusion regarding surface map but what I was trying is that I wanted to create a surface file that contains dice coefficients for labels across the entire cortex. With your response, I think I can get the average dice coefficient for each label and hopefully create a surface map that visualizes dice coefficients on brain surface map. Would there be a way to create my own surface map with brain morphometry values that I created? Best, Julia Shin

3 2

Cortical thicknees normalization values
by Gabbo Ramírez García 09 Jul '21

09 Jul '21

External Email - Use Caution Hi freesurfer user. I have been working with some cortical thickness values of a control group to test some changes related to cognitive training. However, I have been hesitating about whether I have to normalize the cortical thickness values (as happens with subcortical volumes and ICV) or not. I have read a little about it and I understood that I could use the ICV or/and mean cortical thickness, but I didn't find a specific criteria to do or not this normalization. Any clue, recommendation, explanation or paper about this will be very helpful. Thanks in advance. *or reposting discussion of this question. Gabriel R.

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