Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Custom Fill does not fill
by Kiley Seymour 02 Apr '12

02 Apr '12

Dear experts I have just completed all of the steps leading up to overlaying retinotopy activation on an inflated brain. I have been able to Make a Closed Path, but unfortunately when I press the Custom Fill nothing happens. Any ideas why this is the case. I have been using tksurfer-sess -c polar -a rtopy.self.lh -s Subject1 Thanks. Kiley

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TRACULA exited with errors
by Carolina Valencia 02 Apr '12

02 Apr '12

Hi FS users I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first command step trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and chech the size. #@# Tensor fit lun abr 2 13:23:46 COT 2012 dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 i686 GNU/Linux trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 Another question is related to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Many thanks, Best regards -- -- *Carolina Valencia M*

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Re: [Freesurfer] coreg error
by Douglas N Greve 02 Apr '12

02 Apr '12

There does not appear to be an error at the end. doug On 04/02/2012 12:58 PM, Borzello, Mia wrote: > mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz > mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... > Starting DICOMRead2() > dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 > dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 > Ref Series No = 6 > Found 138 files, checking for dicoms > Found 136 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 1.25 > Vs: 0 0 1 > Second Sorting > Counting frames > nframes = 1 > nslices = 136 > ndcmfiles = 136 > PE Dir = UNKNOWN (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -1, 0) > k_ras = (-0, -0, 1) > writing to ct.mgz... > ________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Monday, April 02, 2012 10:00 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] coreg error > > Can you paste the terminal output into the email instead of sending a pic? > > On 4/2/12 9:54 AM, Borzello, Mia wrote: > > Morning guys, > > > I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.) > > > > Thanks! > Mia > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Borzello, Mia > Sent: Sunday, April 01, 2012 10:59 PM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] coreg error > > Hey guys, > > When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz > file. but when i use spmregister, it says that spm.reg.dat is > unrecognizable. How can i remedy this? > > Thanks so much! > Mia > > _______________________________________________ > 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<mailto:Freesurfer@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

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Grayscale Histogram Correction
by Jörg Pfannmöller 02 Apr '12

02 Apr '12

Hello @all, I want to segment anatomical data recorded from an experiemental sequence. This sequence creates pictures with contrasts in a rather narrow range around two hundred if projected into an 8bit grayscale. Freesurfer fails to segment those data. However, if I rescale the brightness in tkmedit the pictures have an excellent quality. Can somebody tell me how to correct the grayscale histogram? Regards pfannmoe

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total wm volume
by Ayaz, Muhammad 02 Apr '12

02 Apr '12

Dear All, I used the following command line to extract the volumes from Stats file. asegstats2table --subjects sub1 sub2... --stats wmparc.stats --tablefile aseg_wm_volume.txt ?h.CorticalWhiteMatterVol generated using the above command does not match the volume which I calculated by adding all the 34 cortical wm volumes. I even included the cerebellum volume but the ?h.CorticalWhiteMatterVol still comes out to be higher. eg. lh.CorticalWhiteMatterVol = 201577 manual calculated lh volume (34 cortical region + cerebellum)=186382 Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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trac-preproc exited with ERRORS
by Tetiana Dadakova 02 Apr '12

02 Apr '12

Dear TRACULA experts, for one of my subjects TRACULA preprocessing step exited with errors. Could you please look at the log-file attached. Thank you, Tanja.

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coreg error
by Borzello, Mia 02 Apr '12

02 Apr '12

Hey guys, When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this? Thanks so much! Mia

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Re: [Freesurfer] problem in building cortex mask
by Douglas Greve 02 Apr '12

02 Apr '12

For aparc+aseg, the cortex does not take values 3 and 42. Instead, the cortex is divided into regions of interest that range from 1000 to 1999 (left hemi) or 2000-2999 (right). doug ps. Please post questions to the list and not to us personally. Thanks! On 4/2/12 5:15 AM, lorenzo pasquini wrote: > Hi Douglas, > > thank you for replying. Actually I was wrong, there is no ID problem > for the right cerebral cortex: the ID is 42 in both the aseg.stats > file and in the FreesurferColorLUT table. But the problem in building > the masks persists. I am able to build mask of several brain parts > (amygdala, crebral white matter, hippocampi) but not of the cerebral > cortexes. The command lines I use are: > > mri_binarize --i aparc+aseg.mgz --min 2.5 --max 3.5 --o leftcc.nii > mri_binarize --i aparc+aseg.mgz --min 41.5 --max 42.5 --o rightcc.nii > > I am using freesurfer version 4.3.0_64bit. > Thank you again and kind regards, > > Lorenzo > > *Da:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *A:* freesurfer(a)nmr.mgh.harvard.edu > *Inviato:* Venerdì 30 Marzo 2012 19:07 > *Oggetto:* Re: [Freesurfer] problem in building cortex mask > > what is your command line? > > On 03/30/2012 12:00 PM, lorenzo pasquini wrote: > > Dear freesurfers, > > > > I have a problem in creating masks of the left and right cerebral > > cortexes. The message "found 0 values in range" is displayed and an > > empty mask is created. This is surprising as I am able to build masks > > of the right and left hippocampi and entorhinal cortexes using the > > same command without any problems. Further the satistic file > > aseg.stats indicates me a huge amount of voxels in the cerebral > > cortexes. I am using the segmentation ID 3 for the left cerebral > > corex and 42 or 53 for the right cerebral cortex. I am surprised as > > well to find two different IDs for the same region, 42 comes from the > > aseg.stats file, 53 comes from the FreesurferColorLUT table. Wich ID > > is the right oneto use?Why can I build masks of hippocampal regions > > but not of the cerebral cortexes? > > Thank you very much and kind regards, > > > > Lorenzo Pasquini > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 <mailto:greve@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 <mailto:Freesurfer@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. > > >

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Re: [Freesurfer] coreg error
by Douglas Greve 02 Apr '12

02 Apr '12

Hi Mia, there was no attachment. doug ps. Please post responses to the list and not to me personally. Thanks! On 4/2/12 12:15 AM, Borzello, Mia wrote: > Hey Doug, > > Thanks for the quick response. I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.) > > Thanks! > Mia > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Sunday, April 01, 2012 11:03 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] coreg error > > Hi Mia, we'll need more info on what you did. Please send the command(s) > line you used and the terminal output(s). > doug > > On 4/1/12 10:59 PM, Borzello, Mia wrote: >> Hey guys, >> >> When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz >> file. but when i use spmregister, it says that spm.reg.dat is >> unrecognizable. How can i remedy this? >> >> Thanks so much! >> Mia >> >> _______________________________________________ >> 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 > >

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correcting pial surface
by Richter, Julia 02 Apr '12

02 Apr '12

Dear freesurfer experts, I have several subjects whose cortical grey matter isn't included in the pial surface. Is there any possibility to correct the pial surface? I added control points to the white matter to bring the regional white matter intensity up, but it didn't change anything in the grey matter. Thanks for your help, Julia

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Freesurfer April 2012