Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Recon-all for multiple cases
by Loong, Spencer 21 Jun '21

21 Jun '21

External Email - Use Caution Hello FreeSurfer specialists, I am new to FreeSurfer and I am trying to learn how to run the basic recon-all command for multiple subjects at once. Could someone help me with what the command would look like to run a folder full of .nii files (e.g., 01.nii, 02.nii, 03.nii, etc). If I only have 8 cores, am I limited to running 8 cases per command, or can I include all of the cases (40) in the command? I’ve run the command for single cases successfully, now I would like set it and forget it. Your help is greatly appreciated, thank you! Spencer Loong Doctoral Student | Clinical Psychology Department of Psychology Loma Linda University SLoong(a)llu.edu CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify me immediately by replying to this message and destroy all copies of this communication and any attachments. Thank you.

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Problem to run recon-all in one subject
by Rosalia Dacosta Aguayo 21 Jun '21

21 Jun '21

External Email - Use Caution Dear Freesurfer's experts I am trying to run recon-all -all in a subject and it seems there is a problem I do not know how to solve. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2 /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2pial -all *ERROR: cannot find /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w* Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-001_ses-BSL exited with ERRORS at Mon 21 Jun 16:45:13 CEST 2021 For more details, see the log file *(there is no log file created)* To report a problem, see http://secure-web.cisco.com/1fl8R1eHZCuzU6FCHJEl-s4FAaPFJk5v8HULKxGhhH_IJIs… rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd ARTICO *rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ ls* fsaverage sub-001_ses-BSL_T2w.nii sub-003_ses-BSL_T1w.nii sub-001_ses-BSL_T1w.nii sub-003_ses-BSL sub-003_ses-BSL_T2w.nii rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ Any idea would be very appreciated. Kind regards, Rosie

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Issues with recon-all hanging
by Michael Datko 21 Jun '21

21 Jun '21

External Email - Use Caution Hello, I have been collecting data on a 7T scanner, with functional EPI data collected with 1.5mm voxels, and I have been having an issue with some of our data where recon-all just hangs after producing only a small amount of outputs. For instance, it might get to a point where it has generated 5-10 of the “lh” left hemisphere outputs in the surf folder, and then appears as if it continues to run for hours or days but no other outputs get produced and eventually the process times out and quits. I estimate that this happens for about 5-10% of the participants we have collected so far. If it doesn’t work for a particular participant, it will do the same thing again if I delete their temporary working folder and any outputs and try to run again from scratch. This is not happening with data from the same participants collected from a 3T scanner with 3mm EPI voxels, with recon-all run at 2mm. The only difference is the resolution of the data and therefore the resolution at which we are running recon-all. Our 7T functional EPI data is collected at 1.5mm resolution, so for those scans we run recon-all at 1mm resolution. Do you have any advice for how to get these participant’s data to finish with recon-all at 1mm? Thank you, Mike Datko

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Research Assistant Position in ECoG Lab (New York)
by Mishra, Akash 21 Jun '21

21 Jun '21

External Email - Use Caution Dear all, The human intracranial EEG (iEEG/ECoG) Laboratory for Human Brain Mapping at the Feinstein Institutes for Medical Research – Hofstra Northwell School of Medicine is looking for one research assistant with earliest start date in July 2021. The successful candidate will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with preparing progress reports and grant applications, and helping to present lab findings at conferences and in journals. In addition, if there is interest, the RA will have her/his own scientific project with dedicated time to work on it. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored lab publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -2-year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>) and Ashesh Mehta (amehta.northwell.edu<http://secure-web.cisco.com/1EUBMRvU22CDa5zzZqplYWfCju5FtyqFJQdEYK6ame8M6ox…>). We are looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Infant FreeSurfer: volumes
by k3ops＠free.fr 21 Jun '21

21 Jun '21

External Email - Use Caution Hi FreeSurfer team, I using the latest version of Infant FreeSurfer to assess brain volumes on very young kids. When looking at the brain volume (aka 'BrainSegVolNotVent') extracted from the aseg statistical file I got a very different volume than doing the pixel count (weighted by pixel resolution). For example: - BrainSegVolNotVent: 1174.5 - PixelCount: 1250.8 With standard FreeSurfer (on adults) I was used to get similar volumes when comparing aseg stat file and pixel count. Is that expected? Why there is a discrepancy between the two way of assessment? I know some other structures are not based on pixel count based on FreeSurfer documentation, but looks like brain volume called 'BrainSegVolNotVent' was not impacted: https://secure-web.cisco.com/1K0DiBqkK6tza56FKjGAoo4Gw5DWfMbyfEne1V4rxz67RM… Thanks. Florent

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Finding equivalent vertices on fsaverage_sym lh and rh surfaces
by Tim Schäfer 20 Jun '21

20 Jun '21

External Email - Use Caution Dear FreeSurfer experts, for the 'fsaverage_sym' template that comes with FreeSurfer, I would like to find a mapping between equivalent vertices (i.e., vertices in the same anatomical position) between the left and right hemispheres. By "equivalent" I mean identical anatomical positions. I noticed, for example, that vertex 500 in the file fsaverage_sym/surf/lh.white and vertex 500 in the file fsaverage_sym/surf/rh.white are not at equivalent anatomical points. I feel this mapping must be documented somewhere or there is an obvious way to get it that I am currently overlooking, so I thought I'd ask here. Thanks in advance, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Problem with rca-config when running recon-all
by Juan Felipe Quinones Sanchez 20 Jun '21

20 Jun '21

External Email - Use Caution Dear Freesurfer team, I am new to Freesurfer. I installed it on my WSL (ubuntu 18.04) following the instructions at: https://secure-web.cisco.com/19NPylFTZm62HJK1A_0s-94uhHZebqqpw9Sitxzpx_bTWo…. I believe that the installation was successful because I get documentation whenever I type a function on the command line. I wanted to run recon-all on a T1 image using the following call: $FREESURFER_HOME/bin/recon-all -s subx -i $t1_img -all where $t1_img = /mnt/c/Users/...../t1.nii.gz Unfortunately I got the following error: rca-config: Command not found. I read a thread (https://secure-web.cisco.com/1H4D7loaV8UEB6OJaKKwdNSc3rqTSamNp7b7KUKBFFvTH3…) addressing this topic and followed the suggested solution. I typed everything manually. I also ran the code directly from the console and from a bash script, both with the $t1_img variable and the original file path but the error persists. I found this code (https://secure-web.cisco.com/1rA78FG6F2-U9A7bR00W9v_d5uE-voxX7qbpwkAvn5xBbo…) supposedly running recon-all and there is a line where the command "rca-config" is used. However, it seems to be not recognized even though the file is indeed located at $FREESURFER_HOME/bin/. I would appreciate any sort of guidance. Thank you, Juan

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a query on gray volume from parcellating data
by Koustav Chatterjee 20 Jun '21

20 Jun '21

External Email - Use Caution Dear Sir/Madam, Could you please tell what does it mean by 'Gray volume' and 'avg thickness' of various structures while we are parcellating cortical surfaces through FreeSurfer and getting 'aparcstats2table'. Thank you for your help. Regards, KC [image: image.png]

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mri_glmfit with pvr
by stdp82＠virgilio.it 20 Jun '21

20 Jun '21

External Email - Use Caution Thanks If I have 4 groups GroupDescriptorFile 1 Title XXX Class G1 Class G2 Class G3 Class G4 Input subj1 G1 Input subj2 G3 Input subj3 G2 Input subj4 G2 Input subj5 G4 .... Are the contrasts below corrected? G1_only_thick 1 0 0 0 G2_only_thick 1 0 0 0 G3_only_thick 1 0 0 0 G4_only_thick 1 0 0 0 G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5 G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5 G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25 Thanks Stefano Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, this thread https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2one… 6/3/2021 10:22 AM, std...(a)virgilio.it wrote: > External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups?My mean concern is how buid the fsgd file. Stefano > Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" <gr...(a)nmr.mgh.harvard.edu> wrote: >Hi Aga, what you have done is correct, no need to include the pvr in the >fsgd. >doug > >Burzynska, Aga wrote: >> Dear all, >> I am trying to make group level analysis of functional data on the >>surface and add per-vertex regressors (PVR, here: cortical thickness) >>into the design. When I view the results I have the feeling that the PVR >>is not really included in the model: >> >> I am using the command: >> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd >>Group1versusGroup2.fsgd --pvr lh.thickness.10.mgh --C >>Group1only_thickness.mat --C Group2only_thickness.mat --C >>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C >>Group1plusGroup2_thickness.mat >> >> where >> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed >>level analysis (combining the runs) for each participant >> fsgd file contains: >> GroupDescriptorFile 1 >> Title Group1versusGroup2 >> Class Group1 >> Class Group2 >> Input 1109 Group1 >> Input 1110 Group1 >> Input 1111 Group1 >> Input 1112 Group1 >> ... >> Input 2280 Group2 >> Input 2282 Group2 >> Input 2283 Group2 >> Input 2284 Group2 >> >> The PVR is a file containing thickness maps for each participant, >>concatenated in the same order as for the functional data. >> >> So there are 2 main regressors (1 factor, 2 levels), but the contrast >>files contain 3 regressors (the third one is the PVE), for instance: >> Group1minusGroup2_thickness.mat contains 1 -1 0. >> >> Does it look correct? >> Should the pvr regressor be included in the fsdg file? How can I do it? >> >> Thank you very much for your help, >> Cheers, >> Aga >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ES… >> >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: http://secure-web.cisco.com/1C61OSNwGFU8-MmX4hWZetUP6ivnpYMPZsypGZ1hSjsNzy-… > > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://secure-web.cisco.com/1SUkt2fsByhbVkrjyleWea7U8vPw7dJUUjO3n73A05t_91l… . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ES…

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Running Freesurfer in the Desktop
by Rosalia Dacosta Aguayo 19 Jun '21

19 Jun '21

External Email - Use Caution Dear Freesurfer's team, I am trying to run FreeSurfer recon-all -all in a folder placed *on my Desktop* and I am having some trouble. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt: No such file or directory. I would greatly appreciate your help. Kind regards, Rosie

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Freesurfer June 2021