Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

RE: [Freesurfer] tksurfer display problems
by Wang, Xin 19 Nov '08

19 Nov '08

We did for one node, and going to up-grade the rest. A simple answer to your question is to up-grade any node you want to run tksurfer. Help it helps. Xin ________________________________ From: Siddharth Srivastava [mailto:siddys@gmail.com] Sent: Wed 11/19/2008 6:37 PM To: Wang, Xin Subject: Re: [Freesurfer] tksurfer display problems Hi Xin, Thanks for the reply. I am contacting you since you mentioned that you are running freesurfer on a cluster. I contacted my sysad regarding this problem, and they want to know if this upgrade has to be dome on every node of the cluster. can you recommend something regarding this? best regards, sid. On Wed, Nov 19, 2008 at 11:46 AM, Wang, Xin <Xin.Wang(a)utoledo.edu> wrote: We just solved the same problem by upgrading the driver of video card on the cluster. An early massage in the freesurfer archive gives more details. Xin ________________________________ From: Siddharth Srivastava [mailto:siddys@gmail.com] Sent: Wed 11/19/2008 1:21 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display problems Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow <mjp(a)mit.edu> wrote: Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.ht… Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the "client", in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the "-x" flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran "ldconfig -v" to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with "TLS" (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Version Discrepancies in Cortical Thickness Analysis?
by Ryan Scotton 19 Nov '08

19 Nov '08

Hi Bruce, My team has recently begun planning for data analysis after completing the overwhelming majority of our FreeSurfer runs and manual edits. However, it came to my attention that we do not currently have Qdec installed on our system...I realized that this is because we were using a very outdated version of FreeSurfer (3.0.4) that did not include Qdec. We have since downloaded the newest version so that we can begin data analysis, but this raises a bigger question: is it necessary for us to rerun FreeSurfer on all of our subjects (250+) if we are ONLY concerned with the white matter/grey matter surfaces and cortical thickness measurements? If not, spectacular. If so, is there only a small portion of the recon-all stream that we could run so that we could take care of this problem as fast as possible? Thanks! Ryan

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Issues with FreeSurfer and Slicer3
by joel bruss 19 Nov '08

19 Nov '08

I must have posted this to an incorrect address before so I'll try this again: Hello- I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11. I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were: mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze (The new Analzye set was renamed FSParcel.hdr/img) After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran: mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest (I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well) I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests) tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work? -Joel

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tksurfer display question II
by j janssen 19 Nov '08

19 Nov '08

i´ll rephrase my question: can one display "filled" labels and other "outlined" labels at the same time in tksurfer? see my current attachment (made with help from Gimp..): surface+curvature+aparc (outlined)+some label (filled)+some label (filled). mri_annotation2label will give me labels, fine, but it won´t solve my rephrased question, i think. appreciate your help! -joost Or do you want the separate units to have separate colors? If that's your > goal you can use mri_annotation2label to turn all the parcellation units > into labels and only use the 2 (or more) that you want. > > > cheers, > Bruce > > On Wed, 19 Nov 2008, j janssen wrote: > > Hi Bruce, >> >> to be 100% sure that you guys understand what i want, i have attached the >> same attachment as before but now i quickly manually-painted in some >> regions >> using Gimp. Now, obviously i would like to do this not-manually and within >> FreeSurfer. is this possible? >> >> >> you can use the "custom fill" tool to fill up to other labels. >> >> >> how can i use "custom fill" to fill up a specific label, making it visible >> in tksurfer while keeping the other labels in 'outlined' status? >> >> >> >> You can also start with "all marked vertices" and click in a number of >>> regions, then save them as a label (you can change its color with the >>> "change label color" button on the 2nd row of icons near the right). >>> >> >> >> with "its" you refer to 1 label representing "all marked vertices" for >> which >> the color can be customized. look at the attachment, this is not what i >> would want. maybe i´m missing something obvious, apologies. >> >> -joost >> >> >> >>> >>> On Wed, 19 Nov 2008, j janssen wrote: >>> >>> Hi, >>> >>>> >>>> using version 4.0.5 >>>> >>>> look at the attached picture. its the result of: >>>> >>>> tksurfer code lh inflated -aparc aparc -gray >>>> >>>> i have selected one region (yellow outline). i would like to >>>> - fill this region and some other regions, *but not all regions*! >>>> - give the filled regions different color-labelings >>>> - i would like to display them (outlined and filled regions) at the >>>> *same* >>>> time. >>>> >>>> i have tried numerous ways, without result. any suggestions? >>>> >>>> thanks, >>>> -joost >>>> >>>> >>>>

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tksurfer display question
by j janssen 19 Nov '08

19 Nov '08

Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labelings - i would like to display them (outlined and filled regions) at the *same* time. i have tried numerous ways, without result. any suggestions? thanks, -joost

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mri_surf2surf - Error
by Alexandru Hanganu 19 Nov '08

19 Nov '08

Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10.mgh file with the mri_surf2surf command. We used this command line: mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help. Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.

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recon-all -long questions
by Mishkin Derakhshan 18 Nov '08

18 Nov '08

Hi, I have a couple questions regarding the -long option. 1) The longitudinal instructions listed in recon-all -help all use recon-all -all -long. If I am only interested in the subcortical segmentation, will the longitudinal processing still work if I only use recon-all -subcortseg ? 2) How long does the longitudinal pipeline take for a) tp1, which has already had the cross-sectional workflow run b) tp2, which gets compared to tp1. I suspect a) and b) are the same, but do they take the same amount of time as a conventional cross sectional run? thanks, mishkin

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Configure thresholds in overlay options
by Juranek, Jenifer 18 Nov '08

18 Nov '08

Hi, Running FSv405 on RHEL5. Is any descriptive information available for threshold options in the configure overlay display gui? Specifically the bases for linear, linear opaque, and piecewise thresholds? Visually, the three options appear dramatically different. Are there specific datatypes each overlay option is designed to handle? Many thanks for any information you can provide, Jenifer

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(no subject)
by Al-Radaideh Ali 17 Nov '08

17 Nov '08

Dear FreeSurfer expert, Any way that I can convert the mgz back to any analyze format so that different softwares can open it?. if not, any software that can open the mgz other than freesurfer? Many thanks Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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RE: [Freesurfer] RE: for cortical thickness
by Zhang, Xiaochu (NIH/NIDA) [F] 17 Nov '08

17 Nov '08

This mask is from functional group analysis. Before I did do group analysis, I have to transfer all individual data into standard space. Therefore, there is no special reference for this mask. The only reference whole brain data is the standard talarich dataset in AFNI. I know if I want to get a perfect anatomical ROI mask, I should draw it based on the subject's own T1 data. However, because I want to run a functional and anatomical combined study, I prefer to use one exactly standard ROI from funcitonal result although it has high variability. Usually, in this case when I do a ROI analysis, I will transfer the ROI from the standard space back to the individual space. Please feel free to contact me if you still have some questions about the ROI mask. Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 2:37 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Subject: RE: [Freesurfer] RE: for cortical thickness can you send the file from which ROI5.nii was created? we would need something, even if it is a functional scan, that shows the whole brain, so that we have a reference of just where the mask voxels are located in the brain. our surface tools do not work directly with talairach coords because those coords have such high variability (that can off by as much as 2cm, or more). On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > Thank you so much for your response, Nick! > I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in > Talarich space. > Actually, it is from my group functional data. So I did not have > corresponding T1-data. > > BTW: when can I read the web page describing the steps taken to get > cortical thickness from an ROI defined by a volume mask? I hope I can > read it ASAP. If it is possible, could you please do me a favor and > send the draft to me? > Thanks, again! > > > Xiaochu Zhang PhD > > Visiting Research Fellow > > Neuroimaging Research Branch > > National Institute on Drug Abuse - IRP > > Biomedical Research Center > > 251 Bayview Blvd. > > Suite 200 (NIDA) > > Baltimore MD > > 21224 > > Tel: 443-740-2619 > > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Monday, November 17, 2008 12:59 PM > To: Zhang, Xiaochu (NIH/NIDA) [F] > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] RE: for cortical thickness > > Xiaochu, > > I'm putting together a web page describing the steps taken to get > cortical thickness from an ROI defined by a volume mask. Can you send > me these two files so that I can make sure the steps work correctly? > > 1) the ROI mask file (what you are calling 'abc.nii') > 2) the T1-weighted anatomical volume of the subject from which abc.nii > was created. i need this file to register to a template volume. > > You can post those files (available only to me) by uploading to our > file > drop: > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Nick > > > On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > > Hi, FreeSurfer export, > > > > Thank you very much for response! > > Now, under some export's help, I used to the mri_surf2vol to > > transfer > cortex thickness into nifti. > > The below line is what I used. > > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon > > --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii > > > > I checked the result and found the voxel outside the gray matter is > always zero and in the gray matter is about 0-3. Could you please do > me a favor and tell me whether these data is cortex thickness or not? > > If they are cortex thickness, why are they always different. In my > mind, it should be same in one direction because we calculate the > distance between the white matter line and the gray matter line. > > > > Thanks a lot! > > All the best, > > Xiaochu > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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Freesurfer November 2008