Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

QDEC vs. Command Line Stream
by Arsenije Subotic 24 Apr '18

24 Apr '18

External Email - Use Caution Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to be the consensus when it comes to using QDEC as opposed to using the command line stream? I've seen QDEC used plentifully in the literature, but I am also aware that it has less glm capability. Thank you for any input! Arsenije

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Re: [Freesurfer] FSGD design for multi-centre study
by C.P.E. Rollins 24 Apr '18

24 Apr '18

Hi Douglas, Thanks for your response. I just wanted to confirm how the FSGD and contrast files might look for the multicentre study. If I'm to create a separate class for each combination of diagnosis, sex, and center, would there then be 24 classes? (as there are 2 diagnoses (patient vs. control), 2 sex, and 6 centres). For instance: GroupDescriptorFile 1 Group control_Male_centre1 Group control_Female_centre1 Group control_Male_centre2 Group control_Female_centre2 Group control_Male_centre3 Group control_Female_centre3 Group control_Male_centre4 Group control_Female_centre4 Group control_Male_centre5 Group control_Female_centre5 Group control_Male_centre6 Group control_Female_centre6 Group patient_Male_centre1 Group patient_Female_centre1 Group patient_Male_centre2 Group patient_Female_centre2 ... Then, my contrast between patients and controls would look like 1 1 1 1 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 for a doss model, if I'm additionally controlling for age, or 24 zeros (instead of 1) for a dods model? Moreover, should I expect any issues with using such a high number of classes? Thanks again, Colleen

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Template recon-all register correction, help needed
by Ting Li 24 Apr '18

24 Apr '18

Hi Freesurfer Experts, I had generated my own template and want to register my subjects into this template. Before the registration, I had run recon-all on my template Once I opened it in freeview, I get something like this. I definitely need to correct these surfaces. Could you give me some suggestions about the areas I pointed out? I am really get lost about them. Thanks a lot. If there has more information about using own template, please send them to me. I am really appreciate your help. Best wishes, Ting

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mri_convert
by Timothy Hendrickson 24 Apr '18

24 Apr '18

External Email - Use Caution Hello, I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker which is a tool that emulates a docker environment but does not require root user privileges in order to do so. Anyway long story short when I attempt to run the udocker container of freesurfer 5.3.0-HCP with the default backend (PRoot) I receive a mmap error with mri_convert which reads: PROT_EXEC | PROT_WRITE. I am able to work around this error in certain instances, but that is not important here. What is important is that when I run a udocker container with freesurfer 6 mri_convert runs without issue. My two questions are: 1) What differences exist between mri_convert between freesurfer 6 and 5.3.0 - HCP 2) Is there any way that I can download/install the newer version of mri_convert used for freesurfer 6 within 5.3.0 - HCP? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay)

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mris_convert Segmentation fault.
by Xiuyi Wang 24 Apr '18

24 Apr '18

External Email - Use Caution Hi, I am planning to convert an ASCII file to a gifti file using mris_convert. I am using FreeSurfer 5.3 on Linux 9 stretch. The ASCII file includes the vertex id , its MNI305 coordinates and p value. Vertex id is 0-based, from 0 to 20483. I used fsaverage5 as the template and extracted the coordinates of each vertex on that surface using the following commands. SW = SurfStatReadSurf({[template_path 'fsaverage5/surf/lh.white'],[template_path 'fsaverage5/surf/rh.white']}); coordis = SurfStatInd2Coord(vertex_id, SW) Then I typed mris_convert file_SW.asc lh_SW.gii # because I learnt that generally surface files starts with a hemisphere specifier. or mris_convert file_SW.asc SW.gii The error message is ERROR: MRISalloc: nfaces=-36 < 0. I guess one possible reason is the first coordinate of the first index is negative (-36). So I generated a new file, replacing all the negative x coordinates with its absolute value - unthreshold_file_SW_abs.asc and then typed: mris_convert SW_abs.asc SW_abs.gii This time the error message is Segmentation fault. Could you please give me any clue how to solve this problem? I also tried this command and it works well, suggesting I can use mris_convert smoothly. mris_convert -v lh.white lh.white.neighbors.asc # Many thanks in advance, Xiuyi Wang

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correcting deffect
by Z Hessam 24 Apr '18

24 Apr '18

External Email - Use Caution Hello FreeSurfer Team i have problem when run a data set, i re-run it but that error remain (just "convex hull" changed from 6148 to 6147!!) this is the last line in terminal (that process doesn't exceed that after about 10 hours!!!) "CORRECTING DEFECT 0 (vertices=21958, convex hull=6147, v0=0)" but the first time i run this data set, there was more another line in terminal: "XL defect detected ..." now i want to know why this error occurred ? and what should i note in my data to never encounter this error again? (I read some similar mails, but i didn't understand my questions) thanks a lot again for your attention

2 1

mris_convert Segmentation fault.
by Xiuyi Wang 24 Apr '18

24 Apr '18

External Email - Use Caution Hi, I am planning to convert an ASCII file to a gifti file using mris_convert. I am using FreeSurfer 5.3 on Linux 9 stretch. The ASCII file includes the vertex id , its MNI305 coordinates and p value. Vertex id is 0-based, from 0 to 20483. I used fsaverage5 as the template and extracted the coordinates of each vertex on that surface using the following commands. SW = SurfStatReadSurf({[template_path 'fsaverage5/surf/lh.white'],[template_path 'fsaverage5/surf/rh.white']}); coordis = SurfStatInd2Coord(vertex_id, SW) Then I typed mris_convert unthreshold_file_SW.asc lh_unthreshold_SW.gii # because I learnt that generally surface files starts with a hemisphere specifier. or mris_convert unthreshold_file_SW.asc unthreshold_SW.gii The error message is ERROR: MRISalloc: nfaces=-36 < 0. I guess one possible reason is the first coordinate of the first index is negative (-36). So I generated a new file, replacing all the negative x coordinates with its absolute value - unthreshold_file_SW_abs.asc and then typed: mris_convert unthreshold_file_SW_abs.asc lh_unthreshold_SW_abs.gii This time the error message is Segmentation fault. I have attached the ascii file. Could you please give me any clue how to solve this problem? I also tried this command and it works well, suggesting I can use mris_convert smoothly. mris_convert -v lh.white lh.white.neighbors.asc # This command works well. I generated lh.white.neighbors.asc, suggesting my preparation work is good. Many thanks in advance, Xiuyi Wang

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Surface projection w/ FLIRT Coreg
by Lauren Beard 23 Apr '18

23 Apr '18

External Email - Use Caution Hi FreeSurfer Team, We would like to project functional volumes to an FS average surface in a number of large datasets (several thousand scans). We have already calculated and conducted detailed QA on co-registrations from the functional to structural image using BBR in FLIRT, and would like to use these transforms (in .mat format) rather than re-calculating them. We have already run FS on all images as well (using version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0). Is there a way to use the pre-computed co-registration in the .mat file to project the functional data to the surface without re-computing a new co-registration with bbregister? Thanks for your help! Lauren Beard Brain Behavior Lab

2 1

curv to label
by Christiane Jockwitz 22 Apr '18

22 Apr '18

External Email - Use Caution Dear FreeSurfer experts, I would like to extract some surface values from the Cognitive Ontology maps from Yeo and collegues (2015). These maps are available in terms of curvature files. However, I would need them in terms of labels or annotations. Is there either the possibility to download these maps as label files, or otherwise is there a possibility to convert them into label files? Thank you very much in advance. Best Christiane -- Dr. rer. medic. Christiane Jockwitz Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin INM-1 Forschungszentrum Jülich Tel: 02461-61-85040 Email: c.jockwitz(a)fz-juelich.de Arbeitsgruppe Konnektivität im menschlichen Gehirn C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Klinik für Psychiatrie, Psychotherapie und Psychosomatik RWTH Aachen ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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ERROR: nu_correct
by Dusan Hirjak 22 Apr '18

22 Apr '18

External Email - Use Caution Dear Freesurfer Experts, I am having trouble with recon-all (Freesurfer 6.0). After running a shell script on my subjects I get the following error: Iteration 1 Fri Apr 20 13:22:37 CEST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14731/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.14731/nu0.mnc [XXX.XXX@XXX-pc26:/xxxx/projects/xxxx/main/user/xxxx/subject_c0_200/mri/] [2018-04-20 13:22:37] running: /ropt/freesurfer_6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14731/0/ ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux xxx-pc26 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3 (2017-12-03) x86_64 GNU/Linux recon-all -s subject_c0_200 exited with ERRORS at Fri Apr 20 13:22:37 CEST 2018 Any suggestions what I can do are welcome! Best regards Dusan

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