Freesurfer

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30087 discussions

How to do parcellation in the inflate brain?
by gong jinnan 24 Mar '14

24 Mar '14

Dear FreeSurfer experts, Hello everyone. I am a beginner of Freesurfer. And I want to do parcellation using some templates (are there any accurate templates in surface space?) in the inflate brain after “recon -all” . After that I wish to get some individual areas like M1,SMA and so on in surface space, and then transform then to voxel space. I think it will be more accurate than segment the T1 image in MNI space directly. But unfortunately, after studying for a few weeks I didn’t find a way to do that. So the only way is asking for help…I hope someone could give me some advises or tutorials. If you can help me to solve this problem,I would be very grateful! Sincerely， Jinnan Gong Best wishes for you! Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China

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Difference in volumes btw 5.1 and 5,3
by jh kim 23 Mar '14

23 Mar '14

Dear FS lists When I measured subcortical GM volumes in the same subjects by using both version 5.1 and 5.3, I have observed a considerable difference in volumes between the two versions. For instance, please see the left thalamic volumes below. I cannot figure out why there is much difference between the versions. Which result is more reliable? Left-Thalamus-Proper_5.3 Left-Thalamus-Proper_5.1 10313 9757 8924.8 7746 9834.8 8287 7935.2 7034 8764.1 7747 9411.8 8037 7636.7 8051 9334.7 8255 10024.3 8171 8757.7 6900 9540.9 8316 9294.4 8369 8091 7366 9103.7 7818 9310.2 7974 7583 6872 9838.9 8911 8829.6 8004 9094.8 6973 9492.3 8922 8821.6 7691 7971.6 7376 9901.2 8936 9773.9 8855 9283.7 7615 8801.6 7690 8505.1 7325 8981 7258 9644.7 8860 9104.2 8298 8494.8 7402 9024.9 7721 8117.8 7226 8001.8 7548 8392.3 7668 8606.6 8173 9126.7 7595 8093 7885 8317.7 7157 10556 9307 8669.6 8374 8034.7 7338 8148.5 7276 9048.1 8064 8160.1 7014 8747.9 7894 8329.9 6866 8415.8 8189 9246.9 8256 8194.1 7183 9629.2 9579 7688.2 6398 8349.2 8238 8366.2 7348 8436.5 7616 8372.3 6977 9396.4 7589 9327.5 7684 10001.8 8627 9762.4 9228 8841 8532 8342.4 8024 8645.7 7725 Any comment would be appreciated. Thank you. Kim

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use 1 vs. 2 T1 acquisitions
by Stacey M Schaefer 22 Mar '14

22 Mar '14

Hello freesurfer gurus, We acquire 2 BRAVO T1s on a GE 3T during the same scan session on most of our study participants, but because of various issues, occasionally only get 1 T1/participant. I've been processing the data combining both T1s when we have 2 and using just 1 T1 when that was all we had thinking it would be best to use the highest quality data as possible (more is better rational), especially given the old FS recommendation that multiple acquisitions were better. However, after perusing recent course materials, I came across the suggestion in one of the powerpoints to always be consistent across subjects using either 1 or 2. Is that the most recent recommendation - if we don't have 2 acquisitons on everyone to pick the one with best contrast and only use 1 T1/participant? If so, can you explain why? Thanks for your advice! Stacey Schaefer -- --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321

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Calculating Total White Matter
by Adeyemi, Elizabeth (NIH/NIMH) [C] 21 Mar '14

21 Mar '14

Hello, I need assistance calculating Total White Matter. Can I simply add Cortical White Matter + Unsegmented White Matter (given in the aseg wmparc output)? Thanks Elizabeth Adeyemi

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Anonymizing Siemens DICOM files
by Caspar M. Schwiedrzik 21 Mar '14

21 Mar '14

Hi Freesurfer Experts, we are looking for a good way to remove subject names and dates of birth from Siemens DICOM headers. Is there something implemented in Freesurfer? Matlab's Image Processing Toolbox has a function to anonymize DICOM files ( http://www.mathworks.com/help/images/ref/dicomanon.html) but we later run into trouble with unpacksdcmdir when we use that. Thanks, Caspar

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Re: [Freesurfer] Segmentation fault:11 with mris_anatomical_stats
by Rupa Sabbineni 21 Mar '14

21 Mar '14

muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11 On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni(a)mrn.org> wrote: > Good morning! > > > I was trying to run the mris_anatomical_stats command and for some > subjects I keep getting Segmentation fault:11 error. > > Some of the posts in the archive suggested that I run the recon-all > command since it usually means that subjects surfaces are out of sync SO I > RERAN RECON_ALL(which created the stats). Then I reran > the mris_anatomical_stats command and got the segmentation fault again. > > > The command im using is > > mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log > outSUB1_lhVOL2 SUB1 lh > > > A little background on the new.label. We got the label by doing a > regression in qdec at FDR 0.05 which created cluster and peak cluster label. > > > Can anyone please provide me some insight on how to trouble shoot this > problem? > > Thank you! > > Rupa > -- Rupa

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Re: [Freesurfer] localgi make_outer_surface
by Douglas N Greve 21 Mar '14

21 Mar '14

Hi Charnjit, that script is Maria's code I think (which is why it is a good idea to post to the list and not to us personally :-) doug On 03/21/2014 07:28 AM, Charnjit Sidhu wrote: > Hi Doug, > > I think the problem is similar to the following post on the mailing lists: > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29476.html > > I think the error "denied: host hostname is no submit host" is being caused when matlab is requested in the make_outer_surface process, if you can tell me where and how matlab is requested in the process I can then add code to run our script that enables matlab to run on our cluster. > > Thanks > > Charnjit > > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: 19 March 2014 15:14 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] (no subject) > > Hi, I have not idea what is going wrong. I would try goggling that error > msg to see what it means and how it might be fixed > > doug > > > On 03/19/2014 06:32 AM, Charnjit Sidhu wrote: >> Dear freesurfers, >> >> This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster. >> >> We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag: >> >> recon-all -subjid $i -localGI >> >> I know this requires matlab which we have installed on the cluster however we cannot submit matlab within a working node which the submitted node is trying to do, we get the following error: >> >> denied: host "hostname" is no submit host >> >> this message is given when the make_outer_surface script matlab script is submitted within the submitted job. >> >> We have a script that allows matlab to run from within the cluster and have tried to add this as an environment variable to the script: >> >> matlab=matlab_cluster ; export matlab >> source $matlab >> >> But when we add this it still fails with the same error, >> >> Do you know how I can make changed to the script allowing us to run the above script when matlab is called? Or are we missing something from our script? >> >> I have attached the relevant scripts and output sent to me by the user. >> >> Can you help me. >> >> Thanks >> >> Charnjit >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

tkmedit contrast
by Borzello, Mia 21 Mar '14

21 Mar '14

Hi Freesurfers, I recently coregisered a patient and am trying to visualize the electrodes in tkmedit now, but I'm unable to see them very clearly. The CT has 1mm slices, so I don't think there should be anything wrong with the CT. Is there an option on the gui that deals with the contrast? I attached a picture of the max intensity projection that shows wires but no electrodes. Thanks! Mia B.

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Converting volume from fsaverage to subject space
by Omar Singleton 21 Mar '14

21 Mar '14

Hello Freesurfers, I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done? Thanks! Best, Omar

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mris_preproc patch
by N. Medic 21 Mar '14

21 Mar '14

Dear Doug, I would need the mris_preproc patch, however the link provided (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc) is not working. Is there another way of getting the patch (rather than downloading the new version of FreeSurfer)? Best wishes, Nenad *************** that link should work now doug On 02/07/2013 12:53 PM, Uri Hasson wrote: > Dear Doug, > > We’re still using version 5.1 for a pipeline, and need to send > surface-based measures (volume, area, thickness) to a standard space > for whole-brain analysis. I read you had a patched version of > mris_preproc, but the link saw in an online post (below) doesn’t work. > Is there another link to the utility? > > Thanks, > Uri > > D.G wrote: > --- > Hi Tetiana, thanks for the push. I’ve put a new version of mris_preproc > here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > This will implement the fix. > To “install” make a backup of mris_preproc in $FREESURFER_HOME/bin, > then > move the new version. > You should re-run recon-all with -qcache (no need to rerun all of > recon-all). > > doug > ---

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