[Freesurfer] Talairach
Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option which I can apply after correcting the Talairach transform? P.S following the workflow takes me almost 3-4 days for a subject (looking carefully and fixing everything,, am I on the right track? Help, Please Thank You Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Talairach
Hi Sharon, Because the talairach is the second step, when you fix it you really do have to run everything else to have it applied. In terms of how long it is taking - it is a long process, the speed of which is dependent on your computer speed and also on the quality of your data. What type of computer are you running this on? What type of data is it? Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sharon Ruso Sent: Tuesday, July 10, 2007 5:57 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option which I can apply after correcting the Talairach transform? P.S following the workflow takes me almost 3-4 days for a subject (looking carefully and fixing everything,, am I on the right track? Help, Please Thank You Sharon ___ 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
[Freesurfer] sphere registration
Hi I am using the freesurfer Parcellation, modify the obtained parcels to have a small rois. To validate my parcels subdivision into small rois, I need to know the variation of some roi_gravity_centers. Do you think that with the vertex number on the sphere of a subject (after parcellation) is it possible to know the corresponding vertex number in the template (Atlas) sphere ? In other words, from the annotatation file which is basically ?h.aparc.annot where I modified some labels is it possible to have the correspondence on the Atlas sphere (using the vertices and sphere.reg or other)? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] add the gray matter
Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are 110 on the brainmask.mgz volume. On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] add the gray matter
oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files. cheers, Bruc On Tue, 10 Jul 2007, Wang, Xin wrote: Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are 110 on the brainmask.mgz volume. On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_motion_correct.fsl problems
Hi, I'm still having problems with the rawavg.mgz volume being generated with incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able to generate a correctly-oriented rawavg. Our two log files look very different, but I'm not able to figure out the problem by looking at them. To start with, the i_ras, j_ras, and k_ras value for the 00?.mgz volumes are different in each of our log files. Mine also has several warnings in which it says that it cannot read a matfile, and that the hist.orient value is not valid. I've attached the log files. Any suggestions would be very very welcome. Thanks in advance, Cate rawavg.mgz.mri_motion_correct.fsl_jenni.log Description: Binary data rawavg.mgz.mri_motion_correct.fsl_cate.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] export mgz+label to dicom files
Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ 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] export mgz+label to dicom files
I'm not sure what you mean by labels+T1. Also labels can mean a lot of different things (eg, aseg, aparc, label format). Can you be more specific? T. Song wrote: Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] smoothing and monte carlo sim
If the simulation command-line would be the same across the different contrasts and the contrast matrices have the same number of rows, then you do not have to redo the simulation. Why is the smoothing changing if you are using the same fsgd file? Robert Levy wrote: Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems like a valid thing to do), it becomes less clear how to choose the smoothing. Or maybe it is not possible to use the same mc simulation data, because the smoothing turns out to be different. Should I instead use an average of the smoothing values, or maybe use the lowest one? Conceptually it seems like this might make the results less accurate, but in practice is there a certain level of slack in smoothing without sacrificing accuracy? If not, it makes a big difference, because the full simulation will take 6 days instead of 2. The z simulation, which at at least with the level of smoothing we have applied, showed results being much less significant, which is why I'm trying the full mc simulation. Thanks, Rob Just to give you an idea of the variance in the smoothing reported in fwhm.dat for the three contrasts: lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat17.128043 rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat16.675573 lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.202638 rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.771982 lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat14.438915 rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.766636 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MR to MGZ
Thanks for such a prompt reply, Doug. Unfortunately, I still get an error: ===start=== mri_convert -it dicom home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR... no DICOM files found. Exit end== Here are two other errors, when I try -it ge and -it gelx ===start=== mri_convert -it ge /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR... fname_format : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%d.MR fname_format2 : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%03d.MR freadShort: fread failed freadShort: fread failed zero frames specified in file - setting to 1 TR=812505.81, TE=812505.81, TI=812505.81, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): source matrix has zero determinant; matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; end== ==start mri_convert -it gelx /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR... genesisRead(): can't determine file name format for /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR ===end=== Thanks, - Jerry Doug Greve wrote: There appears to be a problem when freesurfer reads in that dicom file. See if this works mri_convert -it dicom /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz Jerry Yeou-Wei Chen wrote: Hello, We have been having difficulties importing GE .MR files into FreeSurfer. We have tried a number of methods: 1) directly importing .MR 2) converting to .IMG via BrainVoyager, then importing .IMG with .HDR 3) converting to .IMG via BrainVoyager and creating .MAT using SPM99, then importing .IMG with .HDR and .MAT 4) renaming .MR to .DCM, then importing .DCM Here is a summary of our problems: 1) autorecon1 exits with error 2) orig.mgz is in wrong orientation; T1.mgz is in correct orientation but a cosine info error arises when loading in tkmedit; brainmask.mgz is in wrong orientation; reconstructed surface is in wrong orientation (i.e. not actually a hemisphere; appears oblique) 3) orig, T1, and brainmask are all in wrong orientation 4) autorecon1 exits with error (in all cases except reconstructed surface, wrong orientation means: C = axial with anterior to the left and right to the top H = sagittal upside-down S = coronal with superior to the left) Here is a summary of what seems to be the source of our errors, from corresponding recon-all.log files (I have attached .doc and .txt files with longer excerpts) 1) mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform MRIresample(): source matrix has zero determinant; matrix is: -0.000 0.000 -0.000 0.000; 0.000 0.000 0.000 -15877550310885762478336514187067392.000; 0.000 -0.000 -0.000 -2013832203448376356765696.000; 0.000 0.000 0.000 1.000; 2) mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz - INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file 3) reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img... WARNING: analyzeRead(): matfile /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. - INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in
Re: [Freesurfer] export mgz+label to dicom files
OK. Say, I have a label file saved from a user defined ROI in tksurfer (ascii label). I superimpose the label with a T1.mgz file in tkmedit. Now I get a T1 weighted image with predefined ROI highlighted. Can I save the whole series to a nifti or mgz file? Thanks! Tao Doug Greve wrote: I'm not sure what you mean by labels+T1. Also labels can mean a lot of different things (eg, aseg, aparc, label format). Can you be more specific? T. Song wrote: Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ 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] smoothing and monte carlo sim
Hi, That's a good question. I have no idea why changing only the contrast (and changing nothing anatomical) should result in the smoothing being different. I also learned that previous research assistants in our lab encountered the same exact issue but they didn't solve it. My best guess is it is that some randomness that results from average7 being incompatible with an operation along the stream, either in stxgrinder, mris_preproc, or mri_glmfit. Thanks, Rob Doug Greve wrote: If the simulation command-line would be the same across the different contrasts and the contrast matrices have the same number of rows, then you do not have to redo the simulation. Why is the smoothing changing if you are using the same fsgd file? Robert Levy wrote: Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems like a valid thing to do), it becomes less clear how to choose the smoothing. Or maybe it is not possible to use the same mc simulation data, because the smoothing turns out to be different. Should I instead use an average of the smoothing values, or maybe use the lowest one? Conceptually it seems like this might make the results less accurate, but in practice is there a certain level of slack in smoothing without sacrificing accuracy? If not, it makes a big difference, because the full simulation will take 6 days instead of 2. The z simulation, which at at least with the level of smoothing we have applied, showed results being much less significant, which is why I'm trying the full mc simulation. Thanks, Rob Just to give you an idea of the variance in the smoothing reported in fwhm.dat for the three contrasts: lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat17.128043 rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat16.675573 lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.202638 rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.771982 lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat14.438915 rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.766636 -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_motion_correct.fsl problems
ok. it seems to be an osx problem. using a more recent version on a mac did not work, but the orientations were fine when i ran it on a linux box. i can just use that machine to do the motion correction for all of these subjects. thanks for your help! -cate Yes, the problem is with the matfile. This is rather strange since we generate the matfile. It might be some interaction with osx. Do you have a linux box your can try it out on? This also looks like it might be a fairly old version, can you download a more recent version and see if it works on osx? doug Catherine Hartley wrote: Hi, I'm still having problems with the rawavg.mgz volume being generated with incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able to generate a correctly-oriented rawavg. Our two log files look very different, but I'm not able to figure out the problem by looking at them. To start with, the i_ras, j_ras, and k_ras value for the 00?.mgz volumes are different in each of our log files. Mine also has several warnings in which it says that it cannot read a matfile, and that the hist.orient value is not valid. I've attached the log files. Any suggestions would be very very welcome. Thanks in advance, Cate ___ 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] smoothing and monte carlo sim
Oh, sorry, you mean the lower-level contrast? Yes, that can definitely cause difference in smoothness at the higher level because it is a totally different input. Robert Levy wrote: Hi, That's a good question. I have no idea why changing only the contrast (and changing nothing anatomical) should result in the smoothing being different. I also learned that previous research assistants in our lab encountered the same exact issue but they didn't solve it. My best guess is it is that some randomness that results from average7 being incompatible with an operation along the stream, either in stxgrinder, mris_preproc, or mri_glmfit. Thanks, Rob Doug Greve wrote: If the simulation command-line would be the same across the different contrasts and the contrast matrices have the same number of rows, then you do not have to redo the simulation. Why is the smoothing changing if you are using the same fsgd file? Robert Levy wrote: Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems like a valid thing to do), it becomes less clear how to choose the smoothing. Or maybe it is not possible to use the same mc simulation data, because the smoothing turns out to be different. Should I instead use an average of the smoothing values, or maybe use the lowest one? Conceptually it seems like this might make the results less accurate, but in practice is there a certain level of slack in smoothing without sacrificing accuracy? If not, it makes a big difference, because the full simulation will take 6 days instead of 2. The z simulation, which at at least with the level of smoothing we have applied, showed results being much less significant, which is why I'm trying the full mc simulation. Thanks, Rob Just to give you an idea of the variance in the smoothing reported in fwhm.dat for the three contrasts: lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat17.128043 rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat16.675573 lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.202638 rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.771982 lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat14.438915 rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat15.766636 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] export mgz+label to dicom files
You can convert the label into a binary mask (mgz or nii) with mri_label2vol. You can really save a base image and an overlay together. doug T. Song wrote: OK. Say, I have a label file saved from a user defined ROI in tksurfer (ascii label). I superimpose the label with a T1.mgz file in tkmedit. Now I get a T1 weighted image with predefined ROI highlighted. Can I save the whole series to a nifti or mgz file? Thanks! Tao Doug Greve wrote: I'm not sure what you mean by labels+T1. Also labels can mean a lot of different things (eg, aseg, aparc, label format). Can you be more specific? T. Song wrote: Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
