Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

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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Re: [Freesurfer] Occiptial flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

Yes the lh.occip.patch.3d is in the surf folder for each subject.

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Occipital flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

In response to my previous question, the command line I was using was mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat When I run this, the terminal output reads : lh.occip.patch.3d no such file or directory. I followed all the steps to create the patch, and saved the file with tksurfer. I don't know what could be going on.

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Using Freesurfer Recon1 with Brainvoyager QX
by Ashley A Presley 31 Oct '17

31 Oct '17

Hello, I am trying to use the skullstripping process of recon 1 to clean up the brains before importing into Brainvoyager QX. I convert the files to nifti in freesurfer then to VMR in Brainvoyager with the nifti gifti plugin. When I do this, however, the brain appears to be rotated and using Brainvoyager's manual spacial transformation makes the problem worse. I've attached a screenshot of the brainvoyager window after importing it through nifti gifti. Specs if needed: System: ubuntu 16.04 LTS Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c [cid:3FB7919ECFAE4272A3D7C63E5E71A258] NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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