Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

It does not always work to extract them from the dicom. You should talk to whoever set up your scans to get the bvals and bvects. doug Antonella Kis wrote: > Hi Doug, > > Thanks again. From where I take the bvals and bvects. I was reading > that if my DICOM files were acquired using a Siemens scanner, then > this information can be extracted from the DICOM headers but I don't > know how to do it. > > > Please help. > > Many thanks. > AK > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 2:11 PM > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > That's almost right. Just specify the subject name and not the full > path. Also, you will need to supply bvals and bvects > dt_recon --i DTI_15.nii.gz --s NPI001 --o > /usr/local/freesurfer/NPI001/DTI_15 > > > > Antonella Kis wrote: > > Hi Doug, > > > > Thanks again for helping. So my question is then: I will pass for --i > > (the input data) the .nii.gz file from the DTI data and the it is OK > > to use for the --s which defines the file of the structural recon a > > file called NPI001 where I have 10 files after recon-all (bem, label, > > mri, surf, stats, etc)? In other words if I will set-up: > > > > setenv FREESURFER_HOME /usr/local/freesurfer > > setenv SUBJECTS_DIR $FREESURFER_HOME > > > > and since my files are in /usr/local/freesurfer/NPI001 I am then doing: > > > > cd /usr/local/freesurfer/NPI001 > > > > Here I have the pre-processed files after recon-all and a file called > > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run: > > > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > > /usr/local/freesurfer/NPI001/DTI_15 > > > > Is this right? > > > > I will try by the time you answer but please let me know if you have > > any objection and/or advise. > > > > Many thanks, > > AK > > > > > > > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, August 31, 2011 1:49 PM > > *Subject:* Re: [Freesurfer]: Error with dt_recon > > > > If you pass it dicom, it will try to extract the bvalues, which is > > where it is failing. > > doug > > > > Antonella Kis wrote: > > > Dear Doug, > > > > > > Sorry but I still have a question about this error: > > > I understood that dt_recon it takes original dicom images as input > > and it generates multiple NIFTI volumes that will be used in later > > steps.So why I need to use the NIFTI as input? > > > > > > Thnak you. > > > AK > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* "fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > > > It's looking for the values in the dicom file (which apparently does > > not have them). Convert the dicom to nifit, then use the nifti as > > input, then pass files with bvals and bvects on the command line. > > > doug > > > > > > Antonella Kis wrote: > > > > > > > > > > > > Dear Bruce: > > > > > > > > I am running the dt_recon: > > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > > SUBJECTS_DIR $FREESURFER_HOME > > > > # cd /usr/local/freesurfer/NPI001 > > > > # dt_recon --i > > > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > > > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > > > > and I am getting the following error: > > > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > > > Can you please give me a hint? > > > > > > > > Thank you. > > > > AK > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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. > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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. > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@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 > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@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 > > > > > > > > -- > 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 > > -- 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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Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

That's almost right. Just specify the subject name and not the full path. Also, you will need to supply bvals and bvects dt_recon --i DTI_15.nii.gz --s NPI001 --o /usr/local/freesurfer/NPI001/DTI_15 Antonella Kis wrote: > Hi Doug, > > Thanks again for helping. So my question is then: I will pass for --i > (the input data) the .nii.gz file from the DTI data and the it is OK > to use for the --s which defines the file of the structural recon a > file called NPI001 where I have 10 files after recon-all (bem, label, > mri, surf, stats, etc)? In other words if I will set-up: > > setenv FREESURFER_HOME /usr/local/freesurfer > setenv SUBJECTS_DIR $FREESURFER_HOME > > and since my files are in /usr/local/freesurfer/NPI001 I am then doing: > > cd /usr/local/freesurfer/NPI001 > > Here I have the pre-processed files after recon-all and a file called > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run: > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > /usr/local/freesurfer/NPI001/DTI_15 > > Is this right? > > I will try by the time you answer but please let me know if you have > any objection and/or advise. > > Many thanks, > AK > > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 1:49 PM > *Subject:* Re: [Freesurfer]: Error with dt_recon > > If you pass it dicom, it will try to extract the bvalues, which is > where it is failing. > doug > > Antonella Kis wrote: > > Dear Doug, > > > > Sorry but I still have a question about this error: > > I understood that dt_recon it takes original dicom images as input > and it generates multiple NIFTI volumes that will be used in later > steps.So why I need to use the NIFTI as input? > > > > Thnak you. > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > It's looking for the values in the dicom file (which apparently does > not have them). Convert the dicom to nifit, then use the nifti as > input, then pass files with bvals and bvects on the command line. > > doug > > > > Antonella Kis wrote: > > > > > > > > > Dear Bruce: > > > > > > I am running the dt_recon: > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > SUBJECTS_DIR $FREESURFER_HOME > > > # cd /usr/local/freesurfer/NPI001 > > > # dt_recon --i > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > and I am getting the following error: > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > Can you please give me a hint? > > > > > > Thank you. > > > AK > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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. > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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. > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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> > <mailto:greve@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 > > > > > > > > -- 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 > > > -- 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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Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

If you pass it dicom, it will try to extract the bvalues, which is where it is failing. doug Antonella Kis wrote: > Dear Doug, > > Sorry but I still have a question about this error: > I understood that dt_recon it takes original dicom images as input and > it generates multiple NIFTI volumes that will be used in later > steps.So why I need to use the NIFTI as input? > > Thnak you. > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu>; > "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, August 30, 2011 3:51 PM > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > It's looking for the values in the dicom file (which apparently does > not have them). Convert the dicom to nifit, then use the nifti as > input, then pass files with bvals and bvects on the command line. > doug > > Antonella Kis wrote: > > > > > > Dear Bruce: > > > > I am running the dt_recon: > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > SUBJECTS_DIR $FREESURFER_HOME > > # cd /usr/local/freesurfer/NPI001 > > # dt_recon --i > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > and I am getting the following error: > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > Can you please give me a hint? > > > > Thank you. > > AK > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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. > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > -- 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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Hippocampal subfilelds label
by Shashwath Meda 31 Aug '11

31 Aug '11

Hi Koen - I am looking at some hippocampal subfield measures on 3T and 7T and noticed that there is a label called "hippocampus" from your recent publications it was unclear what this label exactly meant? Is this a useful subfield measure to be considered for further analysis? What does this particular segment represent? Thanks, Shashwath Meda

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Re: [Freesurfer] Freesurfer surfaces in the original space
by Douglas N Greve 31 Aug '11

31 Aug '11

You'll need to do this in steps. 1. Create a registration matrix R between your axial and conformed data: tkregister2 --mov axial.nii --targ orig.mgz --regheader --reg axial.reg.dat --noedit --s subjectname 2. Get the tkreg vox2ras matrix T from your axial: mri_info --vox2ras axial.nii 3. Compute a new matrix M = inv(T)*R. Put it into a file with the same format as axial.reg.dat (call it axia.crs.reg.dat). Just replace the 4x4 matrix. 4. Convert the surfaces with mri_surf2surf, something like mri_surf2surf ---hemi --subject subjectname --sval-xyz lh.white --reg axial.crs.reg.dat --tval lh.white.axial.crs --tval-xyz doug Navid Shiee wrote: > Hi, > > I need coordinates in col-row-slice space of my axial data. The reason > for this is that I have manually picked landmarks on the cortex in the > axial data space and I want to compute landmark errors for the > generated surface. I work with vtk files. I think after all it is a > simple scale+translation of coordinates, but not sure if freesurfer > provides such a tool. > > I know "mri_label2vol" does this for segmentation image. Is there an > equivalent command for surfaces? > > Thanks a lot for your help. > > > On Wed, Aug 31, 2011 at 12:03 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Navid, it is still not clear what you want. Each surface > coordinate has an xyz. This space that this xyz is in is a > peculiar space defined by FS. You want to use a different xyz > space. It could be scanner space. It could be col-row-slice of > your axial data. Or is it that you just want to visualize the > surfaces on the axial. In that case, you'll have to indicate what > tool you are going to use (you cannot use tkmedit for this -- it > will just conform it to 256^3). > > doug > > > Navid Shiee wrote: > > Hi, > Thanks for your reply. I make an examaple to clarify myself. I > have a 256x256x128 axial image which has 0.83^3 resolution. I > am intrested in generating the cortical surfaces and overlay > it on this image. Freesurfer first converts this image to > 256^3 voxels and 1^3 resolution and then generates the > surfaces. Thus if I want to intersect freesurfer surfaces with > my axial data, I can not because surface is in a different > space. Is there a way to transform the freesurfer surfaces to > 256x256x256 axial space? > Thanks a lot for your help. > > Navid > > / Connected by MOTOBLUR™ on T-Mobile > / > > -----Original message----- > > *From: *Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>* > To: *Navid Shiee <navid(a)jhu.edu <mailto:navid@jhu.edu>>* > Cc: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>* > Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00* > Subject: *Re: [Freesurfer] Freesurfer surfaces in the > original space > > > Hi Navid, what do you mean by "the original image space"? > Ie, what > coordinates do you specifically want? Voxel? Scanner? > doug > > Navid Shiee wrote: > > Dear Freesurfer team, > > > > I have a question regarding Freesurfer surfaces. I > submitted this > > questions to the wiki but did not get any response and I was > wondering > > if you can help me on this issue. > > I am doing some experiments with Freesurfer and would > like to have > > surfaces in the original image space. FS converts > everything to > 1mm^3 > > 256x256x256 grid in the coronal space. I have axial > images which > does > > not have homogenous grid (although it has isotropic > resolution). I > > know there is a command to convert the volumetric structural > > segmentation into the original space but could not find > the command > > for surfaces. I would be very grateful if you can provide me > with some > > information for doing this. > > > > I appreciate your kind help in advance. > > > > Regards, > > > > -- > > Navid Shiee > > Ph.D. Candidate > > Laboratory of MEDical Image Computing (MEDIC) > > Image Analysis and Communication Laboratory (IACL) > > Johns Hopkins University > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > -- > 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 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Navid -- 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

1 0

mri_surf2vol
by Antonella Cappelletti 31 Aug '11

31 Aug '11

Hi all, I don't understand what's wrong with this command line: mri_surf2vol --surfval .curv --hemi lh --fillribbon --template orig.mgz --outvol curv-orig.mgz I tried also to use: mri_surf2vol --surfval .curv --hemi lh --fillribbon --template orig.mgz --outvol curv-orig.mgz the error is always the same: cannot recognize the type .curv (or curv). Where is the problem? Thanks, -- Antonella

2 1

Re: [Freesurfer] Freesurfer surfaces in the original space
by Douglas N Greve 31 Aug '11

31 Aug '11

Hi Navid, it is still not clear what you want. Each surface coordinate has an xyz. This space that this xyz is in is a peculiar space defined by FS. You want to use a different xyz space. It could be scanner space. It could be col-row-slice of your axial data. Or is it that you just want to visualize the surfaces on the axial. In that case, you'll have to indicate what tool you are going to use (you cannot use tkmedit for this -- it will just conform it to 256^3). doug Navid Shiee wrote: > Hi, > Thanks for your reply. I make an examaple to clarify myself. I have a > 256x256x128 axial image which has 0.83^3 resolution. I am intrested in > generating the cortical surfaces and overlay it on this image. > Freesurfer first converts this image to 256^3 voxels and 1^3 > resolution and then generates the surfaces. Thus if I want to > intersect freesurfer surfaces with my axial data, I can not because > surface is in a different space. Is there a way to transform the > freesurfer surfaces to 256x256x256 axial space? > Thanks a lot for your help. > > Navid > > / Connected by MOTOBLUR™ on T-Mobile > / > > -----Original message----- > > *From: *Douglas N Greve <greve(a)nmr.mgh.harvard.edu>* > To: *Navid Shiee <navid(a)jhu.edu>* > Cc: *freesurfer(a)nmr.mgh.harvard.edu* > Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00* > Subject: *Re: [Freesurfer] Freesurfer surfaces in the original space > > > Hi Navid, what do you mean by "the original image space"? Ie, what > coordinates do you specifically want? Voxel? Scanner? > doug > > Navid Shiee wrote: > > Dear Freesurfer team, > > > > I have a question regarding Freesurfer surfaces. I submitted this > > questions to the wiki but did not get any response and I was > wondering > > if you can help me on this issue. > > I am doing some experiments with Freesurfer and would like to have > > surfaces in the original image space. FS converts everything to > 1mm^3 > > 256x256x256 grid in the coronal space. I have axial images which > does > > not have homogenous grid (although it has isotropic resolution). I > > know there is a command to convert the volumetric structural > > segmentation into the original space but could not find the command > > for surfaces. I would be very grateful if you can provide me > with some > > information for doing this. > > > > I appreciate your kind help in advance. > > > > Regards, > > > > -- > > Navid Shiee > > Ph.D. Candidate > > Laboratory of MEDical Image Computing (MEDIC) > > Image Analysis and Communication Laboratory (IACL) > > Johns Hopkins University > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > > 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. > -- 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

1 0

how to threshold a sig.mgh file and binarize?
by Burzynska, Aga 31 Aug '11

31 Aug '11

Dear experts, I cannot find a simple way to threshold my sig.mgh file from a functional group analysis (the file is in the fsaverage space). I would like to binarize it and save as a mask to use it with the --mask flag in the mri_glmfit command (to restrict other analyses to these parts of the cortex. I will be very grateful for your help! Cheers, Aga

2 3

Re: [Freesurfer] mris_ca_label
by Haitao Ge 31 Aug '11

31 Aug '11

Hi Bruce, I want to check the results and do some edit if possible. What is the possible reason? Thanks, Haitao

1 0

mris_ca_label
by Haitao Ge 30 Aug '11

30 Aug '11

2 1

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