Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

fsaverage template appropriate to use with pediatric population?
by Avideh Gharehgazlou 21 Nov '17

21 Nov '17

Hi experts, I have a few questions regarding the use of fsaverage template for my research: 1. Is the fsaverage template appropriate for use with pediatric population? (My sample is 6-16 years of age) 2. What possible errors can be expected ? What could possible alignment errors be? 3. Are there any regions I should expect to have more errors in? Would really appreciate a response, Thanks, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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cuda compile help
by Meij, Henk 21 Nov '17

21 Nov '17

cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env recap: 999 cd /usr/local/freesurfer-gpu.git/ 1001 export PATH=/usr/local/cuda-8.0/bin:$PATH 1002 export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64 1004 make clean 1008 ./setup_configure | tee -a setup_configure.log 1011 ./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda-8.0 | tee -a configure.log 1012 time make -j4 | tee -a make.log 1013 make install [hmeij@n78 freesurfer-gpu.git]$ grep nvcc Makefile NVCC = /usr/local/cuda-8.0/bin/nvcc Q1 what causes this and how to fix, make install fails /bin/install -c fs_spmreg.glnxa64 irepifitvol.glnx64 /usr/local/freesurfer-6.0.0/bin /bin/install: cannot stat Ã¢_spmreg.glnxa64Ã¢No such file or directory /bin/install: cannot stat Ã¢epifitvol.glnx64Ã¢No such file or directory make[2]: *** [install-data-local] Error 1 make[2]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make: *** [install-recursive] Error 1 Q2 no cuda packages, maybe related to Q1 [hmeij@n78 freesurfer-gpu.git]$ ls /usr/local/freesurfer-6.0.0/bin/*cuda* /usr/local/freesurfer-6.0.0/bin/cuda_setup Thanks for any help. -Henk

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Problems after running recon-all ...-qcache
by Rosalia Dacosta Aguayo 21 Nov '17

21 Nov '17

Dear FreeSurfer Developers, I have run recon-all....-qcache after reviewing the recon-all...-all outputs in freeview..... I have been looking into: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc Now it seems that I could have omitted the -qcache...and I am a bit lost with the examples showed in the link. Any one could help me regarding the concatenation and how to created the FSGD file? Taking into account I would like to run a cortical thickness analysis between three groups, how I should run the ANOVA? Finally, should I have into account General Atrophy Measures such as: global average thickness for both hemispheres, only or in combination with estimated global intracranial volume as a nuissance regressors in the design? So = ANCOVA instead of ANOVA. Does anyone have any thoughts on how to trouble-shoot those problems? Kind regards, Rosalia

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bash: /home/aimsl/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory
by 许霄 21 Nov '17

21 Nov '17

Hi, I'm a beginner of freesurfer, I was going through the tutorial step by step in Linux. After 'export FREESURFER_HOME=/usr/local/freesurfer' 1) 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' the interface showed: FREESURFER_HOME /home/aimsl/freesurfer FSFAST_HOME /home/aimsl/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/aimsl/freesurfer/subjects INFO: /home/aimsl/matlab/startup.m does not exist...creating touch: cannot touch '/home/aimsl/matlab/startup.m': Permission denied bash: /home/aimsl/matlab/startup.m: Permission denied ... (same with top) ... (same with top) MNI_DIR /home/aimsl/freesurfer/mni 2) cp $FREESURFER_HOME/subjects/sample-001.mgz . mri_convert sample-001.mgz sample-001.nii.gz this step showed same output with that showed in freesurfer website ... reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... 3)recon-all -i sample-001.nii.gz -s bert -all it showed: bash: /home/aimsl/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory Thanks in advance! Best Xiao

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T1 and brainmask wonky: Pieces of putamen missing
by diana hobbs 20 Nov '17

20 Nov '17

Hello FreeSurfer Developers, I am running Recon1 to check/edit the Talairach and Brainmask. The process exits without error; however, I'm finding issues when I open T1.mgz and brainmask.mgz in freeview. Chunks of putamen seem to be boxed out as white matter, but this is not evident in the other files (orig.mgz or nu.mgz). Please see the attached images. The following is the code I am using: #007 recon-all -autorecon1 -subjid TEST007 -i [T1 file] -T2 [T2 file]; - freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - Linux MSI 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 x86_64 x86_64 x86_64 GNU/Linux - Recon-all.log; see attached. I haven't come across this error in my searches, but I may be using the wrong key terms. Would anyone be able to point me in the right direction or trouble-shoot fixing this? Thank you for your time, Diana <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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% overlap of multiple labels
by Yagmur Ozdemir 19 20 Nov '17

20 Nov '17

Hello Freesurfer experts, I am using the mris_compute_parc_overlap command to compute the % overlap of two labels of the same region. Is there a way to do this for multiple labels? Best Idil

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recon-all on previously segmented volumes
by Mcnorgan, Christopher 20 Nov '17

20 Nov '17

Hi, I’m having some issues generating surfaces for an individual and was hoping that a combination of tools might help. In this particular individual, the skull stripping went fine, but a fairly large proportion of the anterior temporal cortex (primarily inferior) volume is excluded from the data. My hunch is that it has to do with the fairly low contrast present in the images. Nonetheless, I had also worked on the data in SPM which did a fine job segmenting the wm/gm/other voxels when I inspect them as overlays in a program like MRICron. I tried an experiment wherein I used the SPM segmented volumes to create a composite brainmask.mgz where the wm voxels were set to exactly 110, the gm voxels were set to a somewhat lower value (I used element-wise multiplication, so the voxels vary in value, but were around 70-100) and all other voxels were set to 1. The resulting volume looks like a meticulously cleaned brain mask. Unfortunately, recon-all -autorecon-pial didn’t work any better afterwards. So that experiment was a dud. Assuming I can manipulate/combine the images in any manner, is there a way to take advantage of the segmented volumes that I was able to obtain from SPM? If I am going to be processing the data in SPM anyways, it would seem that having this information would make the process of tessellating the white and grey matter surfaces trivial. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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[Talairach failed when striping skull]
by Yi Li 20 Nov '17

20 Nov '17

Hi FS expert, When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks! Best Regards, Yi -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [strip skull for unregistered images] Hi Yi yes, brainmask.mgz is the skull stripped image. And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it) cheers Bruce On Mon, 13 Nov 2017, Yi Li wrote: > Hi Bruce, > > Thanks for the help! Is the skull-stripped image in Brainmask.mgz? > > Another question: since my raw image has gone through B1 correction > and > N3 normalization, will you suggest I omit the nu and normalize step in > -autorecon1? > > Best Regards, > Yi > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, November 13, 2017 10:50 AM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [strip skull for unregistered images] > > Hi Yi > > autorecon1 should do the skull stripping, so there is no need for the > separate mri_mask call. The threshold of '5' is so to preserve edits > in which voxels are turned 'off' (they are set to 1 I believe, but we > reserve > 2-4 as additional 'off' values). > > The masking will not transform the voxel coordinates of the image > > cheers > Bruce > > > On Mon, 13 Nov 2017, Yi Li wrote: > >> >> Dear FS experts, >> >> >> >> I would like to strip skulls from unregistered images which have gone >> through GradWarp, B1-correction, N3 normalization and phantom-based scaling. >> I run the following two commands in freeSurfer: >> >> recon-all -autorecon1 -subjid <subjid> >> >> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz >> >> >> >> My questions are >> >> 1) Currently I use 5 as threshold (-T 5). Is there a guidance >> for the setting of this parameter? >> >> 2) In the output file T1.final.mgz, is the skull-stripped image >> represented in ijk space (image index space) or in XYZ space (via >> transformation matrix)? >> >> 3) If the skull-stripped image is represented in XYZ space, how >> do I get it in ijk space? >> >> >> >> Thanks in advance for the help! >> >> >> >> Best Regards, >> >> Yi Li (PhD) >> >> Senior Computational Scientist >> >> Computational Sciences >> >> The Jackson Laboratory >> >> Farmington, CT 06032 >> >> Tel: 860-837-2156 >> >> >> >> --- >> >> The information in this email, including attachments, may be >> confidential and is intended solely for the addressee(s). If you >> believe you received this email by mistake, please notify the sender >> by return email as soon as possible. >> > --- > > The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

2 4

XL Defect Detected
by Arsenije Subotic 20 Nov '17

20 Nov '17

Dear Freesurfer experts, I was processing one of my subjects, but ran into a problem as a XL Defect was detected. The following output was seen (attached screenshot). From examining all of my volumes it seems that they are tilted a bit, but I'm not sure if that is the reason. Thank you for your help. Best, Arsenije

2 1

Re: [Freesurfer] TRACULA
by Yendiki, Anastasia 19 Nov '17

19 Nov '17

2 1

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