Freesurfer

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30132 discussions

Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Douglas Greve 30 Jul '12

30 Jul '12

Hi Jeni, usually you smooth with surf2surf and include a mask or label to indicate that it should only be smoothed inside the mask/label. mri_glmfit will create a mask from non-zero voxels; if you ask glmfit to smooth, then it will only smooth inside of the mask. If you smooth using surf2surf, then do not smooth using glmfit. doug On 7/29/12 11:49 PM, Jeni Chen wrote: > Now I'm confused... So if I included a mask in my GLM analysis (which > I did), then I should add the -fwhm option in mri_glmfit? If that's > the case, does that mean my -y input file should be unsmoothed to > avoid double-smoothing? > > Jeni > > > On 2012-07-29, at 11:31 PM, Douglas Greve wrote: > >> Mostly yes. The one in mri_glmfit will also do smoothing within a >> given mask by default, but basically they do the same thing. >> doug >> >> On 7/29/12 11:15 PM, Jeni Chen wrote: >>> So essentially the -fwhm option in mri_glmfit does the same thing >>> as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! >>> >>> Jeni >>> >>> >>> >> >> >> 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. >> >

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Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Jeni Chen 29 Jul '12

29 Jul '12

So essentially the -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! Jeni

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converting to mgz error
by Skyler Gabriel Shollenbarger 29 Jul '12

29 Jul '12

Hi, Trying to convert a file to mgz and keep getting a 'document file' instead of the freesurfer mgz file. This is the command I used: mri_convert -ot mgz XXXXXXXX-anat+orig.BRIK freesurfer/mri/orig/001.mgz Any suggestions? Thanks! Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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Smoothing in -qcache and the -fwhm option in mri_glmfit
by Jeni Chen 29 Jul '12

29 Jul '12

Hello Freesurfer experts, Just a question about smoothing. I did recon-all -qcache to get pre-smoothed fsaverage surface at 0, 5, 10, 15, 20 and 25mm FWHM, so for mris_preproc I used the "--cache-in" option (eg. for the *10mm.fsaverage file). When I run mri_glmfit, I see the option "--fwhm". Is this option for those who did not pre-smooth their data so that they can do the smoothing there? If I'm using a *.thickness.10.mgh file (10mm FWHM) obtained from the previously described steps as my input file (--y), then by specifing again a value in --fwhm does it mean I'm 'double' smoothing my data? Jeni ------- Jeni Chen, M.Sc. Agente de recherche Laboratoire de recherche en neuropsychologie de la douleur Pav. Paul-G. Desmarais, Université de Montréal CP 6128, Succ. A, Montréal, QC H3C 3J7 Tel: 514-343-6111 x4359

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pial edit question
by Cat Chong 28 Jul '12

28 Jul '12

Dear Experts, I am occasionally noticing some 'pinching' on the inflated brain surfaces around the temporal lobe pole. When I check the brainmask.mgz files, the raised areas are due to a 'bubble' of pial surface forming on top of pial surface. Upon checking white matter and grey matter boundaries, the pial surface should really not be separated as a "bubble", but should in fact be all one surface. What would you suggest would be the best way to fix this? The white matter seems to be fine. Best Regards, Catherine

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recon-all error
by Soo-Eun Chang 27 Jul '12

27 Jul '12

Hello, I've encountered an error message on a couple of my subjects while trying to preprocess for/run qdec. Here is my info copied from running bugr: FREESURFER_HOME: /export/data1/tools/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Red Hat Enterprise Linux Workstation release 6.3 (Santiago) Kernel info: Linux 2.6.32-131.4.1.el6.x86_64 x86_64 Additional Info: 1) Subject name: NF108_11 (SUBJECTS_DIR: /export/data2/PI/freesurfer_subjects) 2) the entire command-line executed: recon-all -s NF108_11 -qcache 3) the error message generated: please see attached recon-all.log, recon-all.error One thing to note is that this subject's original recon-all -all was done using a previous version of FS while the recon-all -qcache command was run after a version update. I'm not sure if this messed things up, but thought I'd mention it. Thanks in advance for your help! Soo-Eun

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Converting labels to individual volumetric masks
by Antonella Kis 27 Jul '12

27 Jul '12

Dear All, I want to use cingulate bundle as ROIs more exactly mask for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in my diffusion space for each individual subject. Is the following correct: 1) mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt nearest JHU-WhiteMatter-labels-1mm.nii.gz s001_aseg2dif.nii.gz 2) fslmaths /[path to subject]/DATA/s001_aseg2dif.nii.gz -uthr 35 -thr 35 /[path to working directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz 3) fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35 Cingulum_(cingulate_gyrus)_R.nii.gz If I want to run for the cingulate bundle the tractography should I repeat this steps for: 36 Cingulum_(cingulate_gyrus)_L 37 Cingulum_(hippocampus)_R 38 Cingulum_(hippocampus)_L Thank you for your help. Antonella

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WM/Pial surfs Problem with SPGRs from 3T GE
by Thomas Fink 27 Jul '12

27 Jul '12

Hey Experts, As you can see from the picture, the autorecon does not work properly (for WM/Pial surfs) with my files: Especially in the temporal lobes. I am working with the SPGR files of a 3T GE Machine. Is there any way to optimize the autorecon results for SPGRs? (Except the lavish application of CPs.) Best regards Thomas On Mon, Jul 23, 2012 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Questions about correction over 2 hemispheres and MCC > (Reem Jan) > 2. More than two time-points in longitudinal base = Memory > allocation error? (Liz Bowman) > 3. Re: Talairach registration (Mojdeh Zamyadi) > 4. Subcortical segmentations (Jordan Pierce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Jul 2012 21:12:44 +0000 > From: Reem Jan <r.jan(a)auckland.ac.nz> > Subject: Re: [Freesurfer] Questions about correction over 2 > hemispheres and MCC > To: "Watson, Christopher" <Christopher.Watson(a)childrens.harvard.edu> > Cc: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > 3375B664D4A0834FB7D0C15D590A9EF11825DBC1(a)FMHS-MBX1.fmhs.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, J?rgen and Chris > > Thank you for elaborating further. I've gone with a Bonferroni correction > as I had a limited number of tests (a-priori hypothesis). But just out of > interest Chris, you mentioned you found correlations between subcortical > structures, do you have a reference I could look at? The tool that J?rgen > suggested requires we enter a correlation coefficient, so I wondered if I > could use published values or whether I'd need to calculate my own (if so, > could you please recommend a way of doing that in Freesurfer or FSL?) > > Many thanks in advance > > Kind regards > Reem > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of J?rgen H?nggi > Sent: Sunday, 22 July 2012 7:47 p.m. > To: Watson, Christopher > Cc: Freesurfer Mailinglist > Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres > and MCC > > Hi Chris > > Yes there are such tools. Bonferroni oder Sidak test that take into > account the correlated measures. Here you can find these tools > > http://www.quantitativeskills.com/sisa/calculations/bonfer.htm > > Cheers > J?rgen > > > On [DATE], "Watson, Christopher" <[ADDRESS]> wrote: > > > What about, for example, the correlations I've seen in a cohort of > subjects. > > > > In 158 subjects aged 10-19 (both controls and patients), the > > correlation between L & R thalamus is 0.91, and the correlations > > between L & R of caudate, putamen, pallidum, hippocampus, and amygdala > were all 0.75 or higher. > > > > I would think that a Bonferroni correction would be incredibly > > conservative and, in my opinion, just plain wrong because true > > significant diff's would be missed. Is there any principled way of > > dealing with multiple tests that are correlated? > > > > Thanks, > > Chris > > ________________________________________ > > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > > Sent: Saturday, July 21, 2012 12:01 PM > > To: Watson, Christopher > > Cc: Douglas N Greve; freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Questions about correction over 2 > > hemispheres and MCC > > > > Hi Chris, > > > > bonferroni will be overly conservative in that case, but we rarely > > really know the true covariance structure of the data, so we would > > rather err on the side of being conservative. > > > > cheers > > Bruce > > On Fri, 20 Jul 2012, Watson, Christopher > > wrote: > > > >> Hi Doug et al, > >> > >> The 2nd question is something I've wondered about. Doesn't a > >> Bonferroni correction assume that the measures are independent? > >> If so, I think in the case of subcortical structures, it is incorrect > >> to use this method, as e.g. the putamen and pallidal volumes are not > >> independent of one another. > >> If not, and it is acceptable to use when there are dependencies > >> between measures, how do you calculate the FWE? It wouldn't be equal > >> to alpha/n, unless I am misunderstanding something. > >> > >> Thanks, > >> Chris > >> ________________________________________ > >> 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: Friday, July 20, 2012 2:38 PM > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Questions about correction over 2 > >> hemispheres and MCC > >> > >> Hi Reem, it looks like you've done everything correctly (sorry for > >> the null result). As for your second, question, I don't think there > >> is a way other than Bonferroni. You can try FDR, but it makes the > >> interpretation a little messy. > >> doug > >> > >> On 07/19/2012 07:59 PM, Reem Jan wrote: > >>> > >>> Hi Doug > >>> > >>> I hope it?s okay that I double check I?m doing the correction over 2 > >>> hemispheres correctly and ask a question regarding correction for > >>> multiple comparisons. I will briefly describe what I have done: > >>> > >>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20). > >>> > >>> 1.I ran a surface thickness study: > >>> > >>> ?For the ?mri_glmfit? command, I used DOSS and specified a contrast > >>> of > >>> +1 -1 0 (Controls > MA) > >>> > >>> ?I ran a pre-cached simulation with the following command: > >>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos > >>> > >>> ?This simulation should only have corrected for the left hemisphere > >>> as I understand it. My cluster summary text file showed me that a > >>> cluster survived in the insula. I interpreted this as ?controls had > >>> higher grey matter thickness in this cluster located in the insula > >>> than drug addicts?. However, this was only corrected over the left > >>> hemisphere (when I ran the same simulation in the right hemisphere, > >>> nothing survived multiple comparison correction). > >>> > >>> ?I now wanted to correct the lh results for 2 hemispheres. From the > >>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2 > >>> ways, are both of these correct and give the same result? > >>> > >>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 > >>> spaces --no-sim csdbase > >>> > >>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos > >>> --cwpvalthresh 0.025 > >>> > >>> ?No clusters survived the Bonferroni correction over both hemispheres. > >>> So I assume I can no longer report this result? > >>> > >>> 2.I ran a subcortical volume study: > >>> > >>> ?I used SPSS to perform the statistical analysis on each of 14 > >>> subcortical structures (left and right). Is there a good way to > >>> correct for multiple comparisons, apart from Bonferroni, which would > >>> be very conservative? > >>> > >>> Many thanks for your advice. > >>> > >>> Kind regards > >>> > >>> Reem > >>> > >>> *Reem Jan*** > >>> > >>> BPharm (Hons), RegPharmNZ > >>> > >>> PhD Student / Pharmacist > >>> > >>> School of Pharmacy, Faculty of Medical & Health Sciences, The > >>> University of Auckland, Private Bag 92019, Auckland, New Zealand. > >>> > >>> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 > >>> > >>> F: +64 9 367 7192 > >>> > >>> *From:*freesurfer-bounces@nmr.mgh.harvard.edu > >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of > >>> *Douglas Greve > >>> *Sent:* Friday, 20 July 2012 11:52 a.m. > >>> *To:* freesurfer(a)nmr.mgh.harvard.edu > >>> *Subject:* Re: [Freesurfer] slice-by-slice predictors > >>> > >>> Sorry, not possible. > >>> > >>> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote: > >>> > >>> Hi! > >>> Is it possible to have slice-by-slice predictors in Freesurfer, and > >>> if so, how? > >>> Thanks, > >>> Caspar > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> _______________________________________________ > >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > >> _______________________________________________ > >> 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 > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ---------------------------------------------------------------------------- > J?rgen H?nggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > > ---------------------------------------------------------------------------- > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jul 2012 10:21:33 +1000 > From: Liz Bowman <ea_bowman(a)hotmail.com> > Subject: [Freesurfer] More than two time-points in longitudinal base = > Memory allocation error? > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SNT135-W17F702D9DC415BB91613828CDD0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hello, > I have several patients scans taken over multiple time points (up to nine > time points in some patients). I thought I might be able to use these to > create a base template for longitudinal processing, however the process > fails and exits with errors if I try to create a base with more than two > time points from a patient. > This is a sample of the error log of the most recent attempt, with three > timepoints: > Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- > diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. > transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: > 0.00156813 < 0.01 :-) > Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- > diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) > malloc: *** mmap(size=262144) failed (error code=12)*** error: can't > allocate region*** set a breakpoint in malloc_error_break to > debugMRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice > Cannot allocate memoryDarwin 550D-UOM88670.local 10.8.0 Darwin Kernel > Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 > For more details, see the log file > /Applications/freesurfer/subjects/KSx3/scripts/recon-all.logTo report a > problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > I would be grateful for any advice. > Regards, > EA Bowman > > >

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CSF and brain volume quantification.
by Matthew Goldfinger 27 Jul '12

27 Jul '12

Dearest gurus of all things Freesurfer, I am looking for a simple way to quantify the amount of CSF, the total volume of brain matter (excluding ventricular space if possible) and, as a check on these two, the total intracranial area. Essentially I need a way to compare how much room there is for the brain to move around and deform. Any ideas on how best to achieve these goals would be most appreciated. Best, Matthew

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FreeSurfer TrackVis Transforms
by Trietsch, Rayna 27 Jul '12

27 Jul '12

Hi, I would like to follow the workflow for the FreeSurfer TrackVis Transforms (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms) but I'm not sure how to get started. The first step is to load the trk data and divide the trk coordinates from the file by the voxel_size in the header. How do I do that? Is this done in matlab? Is there a way to export the trk coordinates into matlab? If anyone could help me get started with this, that would be great. Thanks. ~Rayna~

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