Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

-normalization all black
by Teo Gelles 03 Jul '14

03 Jul '14

Hi Everyone, I would like to normalize some images. But even when I test the -normalize option with recon-all -s burt/ -normalization which from what I can see changes /burt/mri/nu.mgz (which came with the freesurfer download) to /burt/mri/T1.mgz, T1.mgz is entirely black. Is there a way to fix this issue? Thanks. Teo

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freeview error
by Cooke, Gillian 03 Jul '14

03 Jul '14

Hi All, I was hoping that someone might be able to help me. When I load a surface into freeview (e.g. /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error in my terminal: Did not find any volume geometry information in the surface When I go on to load in my multiple comparisons corrected image the entire surface turns yellow. Any suggestions for a fix? Many thanks, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana

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mkcontrast manual weighting?
by DeCross, Stephanie N. 03 Jul '14

03 Jul '14

Hi, I’m making contrasts, and my 6 conditions are as follows: #1 female approach #2 male approach #3 female withdraw #4 male withdraw #5 car approach #6 car withdraw If I want to create the contrast all-approaching-things minus fixation, I’m dealing with #1 female approach, #2 male approach, and #5 car approach. When I’m making the contrasts with mkcontrast, if I do (-a 1 -a 2 -a 5) that’s not what I want, because Matlab then weights each of them as .333. What I really want is for the car’s weight to equal the combined face’s weight to account for the 2 types of genders but only 1 type of car. Would it be correct to manually weight it as: ( .25 .25 0 0 .5 0)? I’m pretty sure that’s correct, but I just wanted to double check. Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

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MINC_BIN_DIR
by Paras Patel 03 Jul '14

03 Jul '14

HI, I am trying to use recon-all for brain analysis work. I have managed to get 4 of them done, but after being away for a couple of days I not get this error: firstly: MINC_BIN_DIR not defined nu_correct also shows to be missing therefore the analysis does not work. I have searched through the help pages and tried the source /usr/local/freesurfer/SetUpFreeSurfer.csh but i get an error with that also. line 42: syntax error : unexpected end of file Also one of the help pages suggested accessing the BIN folder in freesurfer but I do not have this folder either. Any help would be appreciated, Thanks, Paras

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Re: [Freesurfer] Longitudinal pipeline + LME question
by Martin Reuter 03 Jul '14

03 Jul '14

Hi Brianna, I recommend to run all scans of a patient with one single subject template (base). Then , if you are interested if atrophy rates change after intervention, you could use a piecewise linear model, with a node at the surgery. You can then compare your change in slopes with the change in the control group (without intervention). If you are interested not in atrophy rates, but only if volume or thickness changes, the model would be different, but you still need a controll group to test if what you find is different from control group behaviour. Best martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Brianna Damadian <bdamadia(a)buffalo.edu> Date:07/03/2014 1:57 AM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal pipeline + LME question Hi Martin, Thanks for the response. What we are trying to do is look at changes within the same subject after a certain date (date of a surgical procedure). Would it make more sense to run all scans before and after this date in the same longitudinal pipeline and then look for differences or to run all pre-intervention scans with a separate longitudinal template from the post-intervention scans and then look for differences between the "pre" group as a whole and the "post" group as a whole? We are looking for the method that will give us the least variability due to processing differences. Any input you have would be great. Thanks! > On Jul 2, 2014, at 5:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > > Hi Brianna, > > Yes, that is the best option in my opinion. You should include field strength as a covariate, and maybe other acquisition parameters. > > Best Martin > > > Sent via my smartphone, please excuse brevity. > > -------- Original message -------- > From: Brianna Damadian > Date:07/02/2014 10:04 PM (GMT+01:00) > To: Freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Longitudinal pipeline + LME question > > Hello experts, > > We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, different TR) - not exactly ideal. > > We are looking for changes in total ventricular volume as well as total gray matter and white matter (among others). I am new to this software, but from what I have read in the literature the best approach would be to use the longitudinal pipeline in FreeSurfer and then use the Linear Mixed Effect model (LME) for statistical analysis. In your opinion, is this the correct approach based on our sample/goals? > > Thank you. > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Longitudinal pipeline + LME question
by Martin Reuter 02 Jul '14

02 Jul '14

Hi Brianna, Yes, that is the best option in my opinion. You should include field strength as a covariate, and maybe other acquisition parameters. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Brianna Damadian <bdamadia(a)buffalo.edu> Date:07/02/2014 10:04 PM (GMT+01:00) To: Freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal pipeline + LME question Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, different TR) - not exactly ideal. We are looking for changes in total ventricular volume as well as total gray matter and white matter (among others). I am new to this software, but from what I have read in the literature the best approach would be to use the longitudinal pipeline in FreeSurfer and then use the Linear Mixed Effect model (LME) for statistical analysis. In your opinion, is this the correct approach based on our sample/goals? Thank you.

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Re: [Freesurfer] problems with Surface-based Interhemispheric Registration
by angela.favaro＠unipd.it 02 Jul '14

02 Jul '14

Hi Doug did you see my mail below? any ideas of where the problem could be? thank you! I am using the 5.0, but I have followed the instructions and downloaded the new files as indicated. the xhemi folder has some folders that are empty (bem, label, src, stats, tmp), while the others include files (mri, scripts, surf, touch) Is it possible that the script fails to copy files in the xhemi/label directory? I noted that the script copies other files from the subj00X folders to the xhemi folders, but label files are not copied. May I find the label files in other folders and manually copy them into the xhemi/label folder? which are the correct files? Thank you for your help! Angela > > > I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? > doug > > On 07/01/2014 11:06 AM, angela.favaro(a)unipd.it wrote: >> sure! thank you >> >> >>> Can you send the log file (or the full terminal output)? >>> On 06/30/2014 03:11 PM, angela.favaro(a)unipd.it wrote: >>>> Hi all, >>>> I have a problem with 'Surface-based Interhemispheric Registration' >>>> >>>> I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >>>> >>>> finish with the error below >>>> (indeed in the xhemi/label directory, there is no file) >>>> >>>> What can I do? >>>> Thank you for any help! >>>> Angela >>>> >>>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed >>>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>>> /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n >>>> No such file or directory >>>> mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory >>>> >>>> No such file or directory >>>> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >>>> root:xnu-1504.15.3~1/RELEASE_I386 >>>> i386 >>>> >>>> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST >>>> 2014 >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 > >

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Longitudinal pipeline + LME question
by Brianna Damadian 02 Jul '14

02 Jul '14

Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, different TR) - not exactly ideal. We are looking for changes in total ventricular volume as well as total gray matter and white matter (among others). I am new to this software, but from what I have read in the literature the best approach would be to use the longitudinal pipeline in FreeSurfer and then use the Linear Mixed Effect model (LME) for statistical analysis. In your opinion, is this the correct approach based on our sample/goals? Thank you.

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Processing then xhemi registration to group healthy hemispheres
by Peggy Skelly 02 Jul '14

02 Jul '14

Hi, In our analysis of stroke patients, I've followed the recommendation <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html> to process images, then flip the final surfaces with xhemi for only the subjects with RH lesions to group all healthy hemispheres together for statistical analysis (instead of flipping the initial/raw images prior to processing.) 1 - In documenting the process (and preparing for publication), can you expand upon the reasoning (and possibly point to a reference) for processing prior to flipping? (possibly L-R asymmetries in templates/atlases used in talairach registration, skull stripping, segmentation, parcellation?) 2 - The xhemi reference, Greve et al 2013, explains the symmetric template creation very well. Is fsaverage_sym the template from the ref? (N=42, mostly women) Thanks, Peggy

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Re: [Freesurfer] recon-all CUDA error
by Chiu, Bryan (PHTH) 02 Jul '14

02 Jul '14

Hi, Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly. I think Freesurfer only supports up to CUDA 5.0 so far (although I know Freesurfer group stopped supporting the option and left the flags around). Two options exist: Either in a future patch the program can just be enabled to call the newer version of CUDA (or if I can find where it tries to find CUDA from, edit it to accept any version), or to install any version of CUDA less than or equal to 5.0 To others: The OpenMP and -use-gpu flag are quite promising. I took a recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core processor (i7 4770k). I am currently trying to see if I can speed up faster using the CUDA enabled option. There was a paper titled "Improving the Execution Performance of Freesurfer" which implements a resource scheduler on top of the CUDA and openMP option. No comment on the accuracy of the recon-all using all of these in combination. - Bryan Date: Mon, 30 Jun 2014 16:34:45 +0000 From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A59499D(a)s-itsv-mbx06p.ead.ubc.ca> Content-Type: text/plain; charset="iso-8859-1" Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work. -Bryan Date: Fri, 27 Jun 2014 17:59:37 +0000 From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Subject: [Freesurfer] recon-all CUDA error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A594981(a)s-itsv-mbx06p.ead.ubc.ca> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows: [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial (http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/) With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan

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