Re: [Freesurfer] mri_ca_normalize error
could also be something wrong with running zcat Bruce Fischl wrote: sounds like un.mgz doesn't exist (or you don't have read permission) On Mon, 28 Nov 2005, Michele Perry wrote: Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: === CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR//mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1., y_r = 0., z_r = 0. x_a = 0., y_a = 0., z_a = 1. x_s = 0., y_s = -1., z_s = 0. c_r = 0., c_a = 0., c_s = 0. reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR//mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status === $SUBJECTS_DIR//mri contains nu.mgz and the talairach looks normal. How do I fix this? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_ca_normalize error
sounds like un.mgz doesn't exist (or you don't have read permission) On Mon, 28 Nov 2005, Michele Perry wrote: Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: === CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR//mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1., y_r = 0., z_r = 0. x_a = 0., y_a = 0., z_a = 1. x_s = 0., y_s = -1., z_s = 0. c_r = 0., c_a = 0., c_s = 0. reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR//mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status === $SUBJECTS_DIR//mri contains nu.mgz and the talairach looks normal. How do I fix this? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] motion correction during recon-all
Can you elaborate on what "brings to a screetching halt means"? Is there an error msg or does it just hang? doug Don Hagler wrote: I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.) Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans. My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i\*.1 $destdir/$mgzname.mgz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2
You need to download the talairach subject from the freesurfer website. doug Margo McKenna Benoit wrote: Hi, I am trying to manually check the talairach registration from recon-all using tkregister2, but it appears to be looking for files in talairach/mri/orig. This directory structure does not exist in my dataset. The tutorial recommended the following command line: *tkregister*2 --mgz --s --fstal --surf orig --fstal Check and edit the talairach registration that was created during the FreeSurfer reconstruction. Sets the movable volume to be $SUBJECTS_DIR/talairach/mri/orig and sets the registration file to be $SUBJECTS_DIR/subjectid/transforms/talairach.xfm. User must have write permission to this file. Do not specify --reg with this flag. It is ok to specify --regheader with this flag. The format of the anatomical can be changed with --mgh or --mghz My data is in /space/lucy/2/users/margo/subjects/avm002 and I am using the std environment. Can I run this command without the --fstal? What should I specify as the target and movable volumes in that case? Thank you, Margo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_ca_normalize error
Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: === CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR//mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1., y_r = 0., z_r = 0. x_a = 0., y_a = 0., z_a = 1. x_s = 0., y_s = -1., z_s = 0. c_r = 0., c_a = 0., c_s = 0. reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR//mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status === $SUBJECTS_DIR//mri contains nu.mgz and the talairach looks normal. How do I fix this? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister2
Hi, I am trying to manually check the talairach registration from recon-all using tkregister2, but it appears to be looking for files in talairach/mri/orig. This directory structure does not exist in my dataset. The tutorial recommended the following command line: *tkregister*2 --mgz --s --fstal --surf orig --fstal Check and edit the talairach registration that was created during the FreeSurfer reconstruction. Sets the movable volume to be $SUBJECTS_DIR/talairach/mri/orig and sets the registration file to be $SUBJECTS_DIR/subjectid/transforms/talairach.xfm. User must have write permission to this file. Do not specify --reg with this flag. It is ok to specify --regheader with this flag. The format of the anatomical can be changed with --mgh or --mghz My data is in /space/lucy/2/users/margo/subjects/avm002 and I am using the std environment. Can I run this command without the --fstal? What should I specify as the target and movable volumes in that case? Thank you, Margo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] motion correction during recon-all
I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.) Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans. My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i\*.1 $destdir/$mgzname.mgz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] skull stripping
Dear all, To improve skull stripping, I adjusted the watershed threshold using wsthresh, but this did not work well with our data. Do you have any other suggestions for improving skull stripping when there is too much membrane included? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Script: setfile sulc
> I'll save the tiff question for kevint It's just: save_tiff > >Newbie questions: > > > >I'm doing some stuff inn a script (with the -tcl option in > >freesurfer). This is very nice, but I have problems with the > >following: > > > >1) I don't get the curvature file to work. I've tried with: > > setfile sulc (and then the full path to the file). > > No error, but the files effects isn't being added. > > > >2) Is it possible to save as tif from the script? (I use now: set rgb > > and save_rgb) > > > >Regards! > > > >Henrik Ormåsen > >IT analyselab, Psykologi -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy and FsFast
hi doug i'm not sure how to find out what the version of freesurfer is as the -all-info command doesn't work on csurf. however, the installation tar file i originally downloaded was called: freesurfer-20040218-Linux.tar.gz (for RedHat 9) my paint-sess log says the version of paint-sess is: $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ FAST Version 20031218 are only 3 colours (red=upper field/fovea, blue=horizontal meridian/parafovea, green=lower visual field/periphery) used to specify the polar angle and eccentricity? what should the overlay threshold settings be in tksurfer to correctly display them? thanks! Jane In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > What version of freesurfer (and paint-sess) are you using? This was a > problem in some versions about 6 mo ago, but I thought I fixed them > all. > > doug > > > > On Thu, 24 Nov 2005, Jane Aspell wrote: > > > hi again > > I have been proceeding with the retinotopy analysis using FsFast, following > > the > > instructions at: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > > and i believe i have successfully overlaid the results on my surfaces and > > now > > have two questions: > > > > i wasn't able to create the fieldsign with 'paint-sess' because it couldn't > > find > > tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it to > > use > > tksurfer.old but this doesn't work in the former case. how can i make > > 'paint-sess' use tksurfer.old and thus create the fieldsign? > > > > there are no instructions on how to relate the colours seen when viewing > > eccen > > and polar to the location of the ring and wedge. is there a map somewhere > > that > > can be loaded that tells me what order the colours run from fovea to > > periphery > > and from vertical to horizontal meridian etc.? > > > > thanks again for your help! > > > > jane > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about aseg.stat data
Can you send us the recon-all.log file from the subjects/scripts dir? On Wed, 23 Nov 2005, tulu wrote: Dear freesurfer experts, I use freesurfer and bert data to run recon-all script. It can finish without error. However, when I check the aseg.stats data and find some regions such as inslula or operculum volume are zero. Is it right ? or I should change something other than default setting ? thanks replay Sincerely KL chen -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
