Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

Which command generates the lh.area.pial.fsaverage.mgh file?
by ts+ml＠rcmd.org 22 Oct '18

22 Oct '18

External Email - Use Caution Dear FreeSurfer experts, I would like to know how to (re-)generate the files 'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject (in the surf/ dir). I have tried the following: 1.) ensured that the source files, lh.area.pial and rh.area.pial, exist (under surf/). 2.) run: 'recon-all -s <subject> -qcache -measure area' But this does not generate the expected files (only those for the white surface). Any clues? 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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Re: [Freesurfer] leak of white surface into ventricles
by Antonin Skoch 21 Oct '18

21 Oct '18

External Email - Use Caution Hi Bruce, thanks for the feedback. Orig surface is NOT crossing the ventricle (screenshot: red - white surface, yellow - orig.nofix surface, blue - orig surface). In fact, there appears a topological defect in orig.nofix, which seems to be correctly fixed. It seems that the issue lies in recon-all -white step. I am using v6.0.0 version for this. Antonin Hi Antonin what does the orig surface look like? If it is crossing the ventricle and the orig.nofix is not, then there is a topogical defect that is causing the leakage cheers Bruce On Sat, 20 Oct 2018, Antonin Skoch wrote: External Email - Use Caution Dear experts, in several subjects I am encountering "leak" of white surface into ventricles (see screenshot with enlarged cursor indicating the problematic area). According to my experience, editing of aseg.presurf.mgz or wm.mgz does not help. orig.nofix surface seems OK (without leak into ventricle). Could you please advise how to correct this type of error? I have also uploaded example subject (named white_surface_in_ventricles.tar.gz) to your FTP server so that you can have a look. Regards, Antonin Skoch

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leak of white surface into ventricles
by Antonin Skoch 20 Oct '18

20 Oct '18

External Email - Use Caution Dear experts, in several subjects I am encountering "leak" of white surface into ventricles (see screenshot with enlarged cursor indicating the problematic area). According to my experience, editing of aseg.presurf.mgz or wm.mgz does not help. orig.nofix surface seems OK (without leak into ventricle). Could you please advise how to correct this type of error? I have also uploaded example subject (named white_surface_in_ventricles.tar.gz) to your FTP server so that you can have a look. Regards, Antonin Skoch

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Ask for your help about freesurfer submillimeter reconstruction!
by Nian Rui 20 Oct '18

20 Oct '18

External Email - Use Caution Dear FreeSurfer Developers, I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard…, which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui

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acquisition protocols 3T Prisma
by Ammons, Carla 19 Oct '18

19 Oct '18

External Email - Use Caution Hello. Could you point me to any recommended acquisition protocols specific to longitudinal studies on a 3T Prisma (morphometry and fMRI)? Thanks! Carla Ammons, M.S. Doctoral Candidate | Medical Clinical Psychology University of Alabama at Birmingham

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Problems to run -autorecon2
by Rosalia Dacosta Aguayo 19 Oct '18

19 Oct '18

External Email - Use Caution Dear FreeSurfer team, I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2* It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls brainmask.auto.mgz nu.mgz rawavg.mgz brainmask.mgz orig T1.mgz mri_nu_correct.mni.log orig.mgz talairach_with_skull.log mri_nu_correct.mni.log.bak orig_nu.mgz transforms rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ Best regards, Rosalia

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ERROR: You are trying to re-run an existing subject
by Rosalia Dacosta Aguayo 19 Oct '18

19 Oct '18

External Email - Use Caution Dear FreeSurfer team, I am experiencing an error when trying to run a subject from a different group but with the same number. I would much appreciate your helping here. Regards, Rosalia rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects_controls/001C/mri $ recon-all -sd ~/Desktop/MS_STUDY/subjects_controls -s 001C -i /home/rosalia/D esktop/MS_STUDY/subjects_controls/001C/mri/001.nii.gz -autorecon1 ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects_controls/001C/mri $

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Problems running the three steps from Free Surfer separately
by Rosalia Dacosta Aguayo 19 Oct '18

19 Oct '18

External Email - Use Caution Dear Free Surfer team, I keep trying to run -autorecon2 but it seems that I should have run recon -all -all instead as I am having problems with the names of my subjects and the same error appears once and again and I do not know how I should do it so I do not miss the lables of my participants. I have a sample of 114 participants divided and 3 groups. Every group has numbers from 001 to 038 and they are in different folders such as subjects, subjects_post and subjects_controls. Now, I after visual inspecting that autorecon1 was fine, I am trying to run -autorecon2 and I keep with the same message: *ERROR:* You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. I wonder if I have to change or rename my subjects in order to be able to run autorecon2, or I should begin again with recon -all -all, as it seems I would not have any problem with the names of my participants. I would much appreciate your helping on this. Yours sincerely, Rosalia

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Problems setting the directory
by Rosalia Dacosta Aguayo 18 Oct '18

18 Oct '18

External Email - Use Caution Dear Free Surfer team, Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work. This is how I have my Free Surfer configurated in my computer: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 -------------------------------------------------------------------------------------------------------- As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop Then I try to run the first step (autorecon1) with one subject, and it appears the following error: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 *ERROR: cannot find /usr/local/freesurfer/subjects/001* rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by default, and I am experiencing problems as well. I would much appreciate any help with this basic question. Kind regards, Rosalia

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Computing relative cortical measures maps instead of absolute cortical measures maps
by Angela Martina Mueller 18 Oct '18

18 Oct '18

External Email - Use Caution Hi, I am referring to a paper of Vuoksimaa et al. 2016. The authors used relative instead of absolute cortical measures (cortical thickness and surface area) to compute individual vertex-cognitive ability correlations throughout the cortex. To compute individual relative cortical thickness and surface area maps of each individual subjects, the authors divided the surface area value at each vertex by the total surface area (sum across all vertices for each subject) and subtracted the mean cortical thickness value (for each subject) from the thickness at each vertex. I would like to use the same approach (relative CT and SA maps instead of absolute maps) for one of the projects of our lab. In the Freesurfer mailing list, I found that the command "fscalc" can be used for simple mathematical transformations of mgh files. Therefore my question: Would it be correct to use “fscalc” with the option “sub” resp “div” to compute these relative cortical measures maps for each of my subjects? Thank you for helping me with this question Angela

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Freesurfer October 2018