Freesurfer

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Re: [Freesurfer] Occiptial flattening
by Patricia Stefancin 03 Nov '17

03 Nov '17

Hi again, I ran the command you send and the output is as follows ls cannot access *patch* : no such file or directory

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Re: [Freesurfer] Occipital flattening
by Patricia Stefancin 03 Nov '17

03 Nov '17

Hi Bruce, Here is the command line and the output. mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat MRISread(lh.occip.patch.3d): could not open file No such file or directory mris_flatten: could not read surface file lh.occip.patch.3d No such file or directory

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Re: [Freesurfer] Occipital flattening
by Patricia Stefancin 02 Nov '17

02 Nov '17

Here is the command line and output

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a question for freesurfer "invalid license"
by 风和月光 01 Nov '17

01 Nov '17

Thanks for your efforts on freesurfer. In the process of installing freesurfer, i meet one problem. I have registered an account on https://surfer.nmr.mgh.harvard.edu/registration.html. Then i receipt a e-mail.. I have created a document named "license.txt" in right file and copy license in it. . But when i commanded code "recon-all -s bert -autorecon1", Terminal displayed I also tried the code"tkmedit bert orig.mgz". Teminal displayed I really do not know what's wrong and hope for your help!

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significant of long_mris_slopes
by lanbo Wang 01 Nov '17

01 Nov '17

Dear freesurfer group, Hi! I used long_stats_slopes and code to process my longitudinal data: long_stats_slopes --qdec sub_qdec_long.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-rate --generic-time --stack-rate thickness.lh.aparc-rate.stack.txt mri_glmfit --osgm --glmdir thickness.lh.aparc-rate --table thickness.lh.aparc-rate.stack.txt I got results sig.table.dat in folder of 'thickness.lh.aparc-rate'. I want to ask what's meaning of this results. Is it the significant results or just directly result? All best, Lanbo Wang

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mris_jacobian error while running recon-all -make all
by Anne Park 01 Nov '17

01 Nov '17

Hello, I'm trying to run recon-all after making manual edits with control points (command: recon-all -make all -subjid [sub]), but the recon-all is exiting with errors at the jacobian_white step: ------ Error below: ------ mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match ../surf/lh.white.preaparc No such file or directory mrisReadTriangleFile failed. No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory ------------------------------- I was wondering if you have any thoughts on why this might be happening? I have attached the recon-all.log and recon-all-status.log files, and my FreeSurfer version is freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c. A few things I noticed that I thought might be related: while the recon-all was running I only saw IsRunning.rh in the scripts directory, not IsRunning.lh+rh. Also, in the recon-all-status.log file, it looks like the lh and rh parts of each step are not always occurring together (although maybe they don't necessarily have to?). Thank you! Anne

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(no subject)
by Vidhu Agrawal 01 Nov '17

01 Nov '17

Respected Sir, How can i scoop out or separate only hippocampus from a 3D MRI of whole brain? With regards vidhu agarwal

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Qdec question
by Mohamed Ali Bahri 01 Nov '17

01 Nov '17

Dear Freesurfer experts, I would like to use "Qdec" tool to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists and not the BA stat list. I am wondering if we could do that with "Qdec"? Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)uliege.be

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Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error
by Patricia Linortner 01 Nov '17

01 Nov '17

Hi all, I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B: -hippocampal-subfields-T1T2). For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial brain). Segmentation works in most subjects, but in some subjects the co-registration of the 7T-T2 MRI scan fails. [Despite good scan quality and pre-alignment using Freeview] I was wondering if you had any input/suggestion(s) for fixing this error (e.g. using mri_register)? Thanks, Patricia

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RFC: Changes to nibabel API for .mgh/.mgz files
by Christopher Markiewicz 31 Oct '17

31 Oct '17

Hi all, I'd like to solicit input for the Python interface to .mgh/.mgz files in nibabel[0]. I've recently had cause to dig into this interface (MGHImage[1]), and found that the naming of header fields[2] (analogous to variable names in C structs) is inconsistent with all of my experience with how FreeSurfer refers to these fields in the code (MRI_IMAGE[3]) as well as in the outputs of many programs, such as mri_info. (In fact, the current names seem to reflect the intermediate variables used in load/save_mgh.m and the description of the affine transforms in the FS Coordinates powerpoints[4].) I'm proposing (https://github.com/nipy/nibabel/pull/569) an API change in nibabel, with field names[5] that more closely reflect what I deem to be common FreeSurfer usage (although it does not adhere precisely to the C structure fields). Given that, it was felt that the FreeSurfer community more broadly should have some say in the final API. To put a few specific questions: Do you depend on the current MGHHeader field names? Would you be averse to updating the field names? If not, are there alternatives to my proposal you would find preferable? While I would be willing to discuss in more detail on this list, I don't want to needlessly pollute a support list with discussions of a third party API. If it's convenient, I would prefer responses on the pull request linked above. Thanks, Chris Markiewicz [0] http://nipy.org/nibabel/ [1] https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py [2] https://github.com/nipy/nibabel/blob/2139ce0d24e65a83295bb6b3eaaf005eaeaebb… [3] https://github.com/freesurfer/freesurfer/blob/master/include/mri.h#L157-L252 [4] https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems [5] https://github.com/effigies/nibabel/blob/55c9bf905ec8785617755f900635fc31ba…

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