Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Skull Strip
by Admin 07 Jul '19

07 Jul '19

External Email - Use Caution Dear Freesurfer group： Now,I want generated a brain mask including the brain but excluding the amplified noise regions after skull strip, but I can't find the corresponding command line, so I send this email to you, hoping to get your help. My English is poor, if I make mistakes , I hope you can understand me. Thanks for your help！ Sincerely: Meng Nan Lin Date: 07/04/2019

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error while running pial_lgi for gyrification index
by vittal korann 06 Jul '19

06 Jul '19

External Email - Use Caution Hi FS experts, I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' #-------------------------------------------- #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 /usr/local/freesurfer/subjects/SATM124/surf mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019 For more details, see the log file /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" I never faced this problem before while running gyrification index. To me, it's looks bizarre. Would appreciate any help. Thanks & regards -Korann

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Re: [Freesurfer] recon-all Error : inputs cannot have multiple frames.
by Yueming 05 Jul '19

05 Jul '19

External Email - Use Caution My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? My inputs' format is dicom,when it is about 200kB,the software can run and has no such error.but when the dicom is more than 500kB,the next error will happen: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames My English is so bad that you know...... Forgive me,please! WISH TO YOUR TEACHING AND REPLY. From a graduate student of China Liaoning University .

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rostral anterior cingulate fix?
by Zeng,Victor (BIDMC - Psychiatry) 05 Jul '19

05 Jul '19

Hi Freesurfer group - I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm seeing a misparcellation of the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta deprecated), and it doesn't seem inappropriate to use control point fixes. How would you best fix this (I'm open to using freeview), without just editing the aparc+aseg.mgz? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] Error in mris_convert thickness file from ascii format
by Jee Su Suh 05 Jul '19

05 Jul '19

External Email - Use Caution Hi Bruce, I obtained the curv vector and used read_surf.m to get the face lists in lh.inflated for fsaverage. If the faces list was generated as a 327680x3 double, would it be correct to say that the number of faces is 327680 as the input argument for write_curv.m? Thanks so much for your help, JeeSu -- Date: Thu, 4 Jul 2019 12:56:57 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in mris_convert thickness file from ascii format To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1907041253020.916(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi JeeSu which surface you use is irrelevant (we only need one with the right topology). As for converting from ascii back to curv, matlab is probably the easist using read_ascii_curv.m and write_curv.m. You will need to also read in a surface to get the number of faces. Again, any one of the same topology ones should be fine (e.g. lh.inflated for lh.thickness.asc) cheers Bruce

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Change image orientation
by Miguel Ángel Rivas Fernández 05 Jul '19

05 Jul '19

External Email - Use Caution Dear Freesurfer devs, Is possible to change the image orientation of the t1.nii images? In that case, what command should be used?. I would like to change them from a LPI orientation to a RAI orientation. Best regards, -- *Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Error in mris_convert thickness file from ascii format
by Jee Su Suh 04 Jul '19

04 Jul '19

External Email - Use Caution Hi Bruce and Doug, Thanks for your responses. Apologies if my query was unclear. The operation I would like to do is the opposite: instead of converting *to* ascii, I want to convert *from ascii to curv format.* I used the command stated in your replies to do the first conversion to ascii, which I required in order to carry out an algorithm for correcting for site effects on the dataframe of vertex-wise thickness values. Now that I have done that, I was hoping to convert back into the original curv format in order to carry out the normal group comparison pipeline (mri_preproc, mri_glmfit). Is this possible, from your view? A slightly tangential note: when I did the first conversion to the ascii format, I used lh.inflated as the surface-- would this have had a significant impact on what I am attempting to do now? Thanks for your help, JeeSu -- Date: Wed, 3 Jul 2019 18:51:49 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in mris_convert thickness file from ascii format To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1907031851200.2160(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi JeeSu if you look at the help for mris_convert, you'll see this example: Convert a scalar overlay file in "curv" format to ascii: mris_convert -c lh.thickness lh.white lh.thickness.asc which you should follow cheers Bruce On Wed, 3 Jul 2019, Jee Su Suh wrote: > > ????????External Email - Use Caution???????? > > Hello, > > I am trying to convert ascii files containing vertex-wise thickness data into binary curvature files > for subsequent smoothing and input into mri_glmfit. The command I used is: > > mris_convert lh.test.asc lh.test.thickness > > > But then get the following error: > > ERROR: MRISalloc: nfaces=-5 < 0 > > > No such file or directory > > > I'm not sure what file or directory the error message is referring to, nor what the meaning of > nfaces is. I am running version 6.0 on macOS Mojave. I have also attached a truncated version of the > ascii file for inspection purposes (the whole thing was too big), which was converted from a csv > that was generated by a python script correcting for site effects. This script took in as input the > original ascii converted from the original lh.thickness file using mris_convert. The coordinates > correspond to the fsaverage template (~160k vertices in the whole file). > > Thanks in advance for any guidance, -- JeeSu Suh, BSc. MSc. Student, Graduate Neuroscience Program McMaster University suhj5(a)mcmaster.ca

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Teach me please!,Looking forward to your reply!
by 月明 04 Jul '19

04 Jul '19

External Email - Use Caution I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? My inputs' format is dicom,when it is 200kB,the software can run.but when the dicom is more than 500kB,the next error will happen: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/18I/mri/orig/001.mgz has 17 frames My English is so bad that you know...... Forgive me,please!

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Trac-all error
by Daniel Callow 04 Jul '19

04 Jul '19

External Email - Use Caution Hello, I am running trac-all preproc with the following code setenv FREESURFER_HOME /Applications/freesurfer_dev source $FREESURFER_HOME/SetUpFreeSurfer.csh *#Must set SUBJECTS_DIR to where data is or else uses what was set up when installing freesurfer* setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons *#Must set up configuration file - see trac-all-config-file in dti_analysis compository* *#In configuration file can change number of subject to perform analysis on each cluster* *#RUN FIRST* trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh *and the attached configuration file. * *However, I get the following error.* #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... TR=9.62, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz... tkregister2 --mov /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz --targ /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat --reg /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:47 EDT 2019 #------------------------------------- /Applications/freesurfer_dev/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Tue Jul 2 18:21:49 EDT 2019 cp /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/base_MCIP0006/dmri/xfms cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat: No such file or directory cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat: No such file or directory Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:49 EDT 2019 *What might be causing the issue? Does it seem like tkregister2 isn't working?* *Thank you for help or assistance you can provide.* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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(无主题) {Disarmed}
by 郑凤莲 04 Jul '19

04 Jul '19

External Email - Use Caution Hi Experts, We want to study the Edinger—Westphal nuclei which is related to oculomotor nerve. Can Freesurfer get its volume or other morphological indices based on MRI images? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Freesurfer July 2019