Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Regarding recon all
by Amar Shukla 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Team, Actually I am trying to test my own data in recon all , but i have taken only one subject for recon. It shows me this error. ERROR! FOV=408.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

2 1

mri_glmfit error
by Ishi Tandon AIB, Jaipur 06 Apr '21

06 Apr '21

External Email - Use Caution Hello FS experts, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir lh.volume.glmdir But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. Could someone please help me resolve it? Thanks for your time. *Regards,* *Ishi Tandon* *B.Tech + M.Tech - Cognitive Neuroscience* *Amity University, Rajasthan*

2 1

fMRIPrep BOLD Output
by Karan Desai 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Freesurfer List, I am running fMRIPrep and getting the first two FS output files (aseg and aparcaseg seen above in the screenshot), but not the actual file I need which is the one where it is resampled to the mesh. I have run fMRIPrep and have those two files except the actual BOLD series resampled to the surface mesh. Is there a FS command that can be used to do that one step? Best, Karan

2 3

quantification of volume of perivascular spaces
by Antonín Škoch 05 Apr '21

05 Apr '21

External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch

2 1

Subthalamic nucleus volume
by T. Pansuwan 05 Apr '21

05 Apr '21

External Email - Use Caution Dear Freesurfer experts, As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted: mri_label2vol —reg $FREESURFER_HOME/average/mni152.register.dat —seg STN-maxprob-thr25-0.5mm.nii.gz —temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz —o STN_mni152_in_mni305.nii.gz But the location was much more dorsal than original, 1) I was wondering if there are alternative methods I should try and what could have been the problem? At the end, I hope to obtain individual subject’s subthalamic nucleus volume, 2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space? Thank you so much! Tanrada Pansuwan

2 1

ERROR: Cannot find stats file
by atacan zeybek 05 Apr '21

05 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a text file of amygdalar nuclei of given subjects. I use this command: asegstats2table --subjects 8070 8071 8077 --statsfile=amygdalar-nuclei.lh.T1.v21.stats --tablefile=amygdalarnuclei.lh.T1.v21.txt –skip And get an error like this: ERROR: Cannot find stats file /home/atacan/Desktop/freesurfer/subjects/8070/stats/amygdalar-nuclei.lh.T1.v21.stats Unfortunately I can't search the mail archives because I get an another error while loading the page. Freesurfer version: CentOS 7 x86_64 (64b) tar archive Platform: Ubuntu 20.04.2 LTS

2 1

functional to anatomical registration question
by Nasiriavanaki, Zahra 05 Apr '21

05 Apr '21

Dear Freesurferers, I have a question and I appreciate it much if you could please reply. I need to know how to check subcortical functional to anatomical registration. I know for checking the cortical registration I can use the below command: tkregister2 --s $subj --mov template.nii.gz --surf --reg init.register.dof6.dat Could you please tell me what command should I use to check the registration in subcortex? 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

Running recon-all with FLAIR
by Edina Szabó 05 Apr '21

05 Apr '21

External Email - Use Caution Dear All, We are running recon-all on the latest version of FreeSurfer (v7.1.1). We are using both T1 and FLAIR images to better define the pial surfaces, but when we run the recommended command line (recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is based on these surfaces), and we get better results without the FLAIR. It seems that FreeSurfer mis-registers the FLAIR to the T1 during the process. Is there a separate step we should do to register FLAIR to T1? Thank you, Edina

2 1

mri_vol2surf empty output
by Karan Desai 05 Apr '21

05 Apr '21

External Email - Use Caution Hi FS Forum, I am posting because after using the command mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf --src bold_preproc.nii.gz --out lh.imagename.nii.gz --regheader sub-01 --trgsubject fsaverage4 -hemi lh I am assuming there are some tags that I may be missing which are leading me to output with empty nii.gz files. The input bold preprocessed files are viewed normally in Freeview, but the output is empty. Thank you in advance.

1 0

Unusual left-right discrepancy of exvivo annot volumes in perirhinal and entorhinal cortices
by Yi Leng Fung 04 Apr '21

04 Apr '21

External Email - Use Caution Dear FreeSurfer Developers, I was examining the perirhinal and entorhinal annot stats from BA_exvivo_thresh.stats when I noted a significant discrepancy between the left and right hemispheres, particularly obvious on the perirhinal volumes. On a set of 40 scans from normal participants, the means of the perirhinal volumes, in mm3, was 79 on the right hemisphere and 738 on the left hemisphere. Further visual inspection of the BA annot files, along with a visual examination of the label files, suggests to me that when both the entorhinal and perirhinal cortices encounter the same vertex, the shared vertex would be assigned to the entorhinal cortex in the right hemisphere. This allocation results in an unusually small perirhinal cortex in the right hemisphere for the annotation files, and consequently a much larger right entorhinal cortex. I did not notice this unusual allocation in the left hemisphere. I am rather unclear on why this should be the case. I am currently using the stable FreeSurfer 7.1 from May 2020 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b). The release notes for version 7.1.1 do not suggest that this specific issue had been addressed, but apologies in advance if it actually had been. I look forward to hearing back from your team. Thank you. Best regards, Yi-Leng

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Freesurfer April 2021