[Freesurfer] mri_vol2vol
Hi Freesurfer experts I am always a little confused with the registration matrices from tracula output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon space, do we use the matrix anatorig2diff.bbr.dat? mri_vol2vol --mov /recon/dmri/dtifit_MD.nii.gz --targ /recon/mri/brainmask.mgz --reg /recon/dmri/xfms/anatorig2diff.bbr.dat --o recon/mri/dtifit_MD_registered.nii.gz Thanks a lot Celine ___ Freesurfer mailing list 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] Tracula - set echo spacing
Hi Anastasia and Tracula experts, We are running a new set of tracula analysis from Bay 6 and are wondering how do we define the number of echo spacing in the dmrirc file. Is it a number that we get from the header of the field map dicoms? set echospacing = ... Thanks a lot Celine -- Celine Louapre, MD, PhD Research Fellow at Massachusetts General Hospital Multiple Sclerosis Imaging Lab AA Martinos Center for Biomedical Imaging Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129, USA ___ Freesurfer mailing list 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] mri_cvs_register using high resolution images
Hi Freesurfer experts I am planing to do a voxelwise group analysis from images acquired at 7T, and I wanted to use the mri_cvs_register script, which gives very nice normalization outputs. I was wondering how to adapt the script to images that we have with 0.33mm isotropic resolution, and which are registered to the FS recon brainmask. I fisrt ran mri_cvs_register on one subject, using the following command: mri_cvs_register --mov subjid --mni --outdir path and then try to apply the registration files to the high res 7T without reslicing (to keep the advantage of the high resolution): mri_vol2vol --mov 7T data --targ $FREESURFER_DIR/subjects/cvs_avg35_inMNI152/mri/norm.mgz --m3z 3T/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o 7T_MNI.nii.gz --noDefM3zPath --no-resample However when I open the 7T_MNI.nii.gz file and cvs_avg35_inMNI152/mri/norm.mgz files using freeview, they are not registered (while the output of mri_cvs_register for that subject was perfectly registered to the template). Would you have an advice to help me on that? Many thanks Celine ___ Freesurfer mailing list 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] TRACULA: distance between tract sections in pathstats.byvoxel.txt
Hi Anastasia and Tracula experts I did analyses with Tracula using the very nice feature that allows to perform the statistics along the tracts. I reported the result as function of location along the tracts expressed as voxel index, meaning that the first section was voxel index 1, the 2nd tract section was voxel index 2 etc along the entire path. However, I just got a reviewer comment asking for the actual distance between each voxel index. I guess this depends on the voxel size, but maybe also on the curvature of the tract? Is there a simple way to have the average distance between 2 sections along one tract? Thank you Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Problem with a recon edit
Thanks Lee, I am testing it right now. Just to be sure, it means that a value of 1 in the wm.mgz volume would be treated differently from a value of 0? I did not touch the wm.mgz volume in those regions because I didn't see anything to delete, but it is interesting to know that even if the sulci were already with a value of 0 in the WM.mgz, it can be helpful to change it to 1. Thanks a lot for the tips (and also the visualization tip, super helpful :-) Celine Hi Celine, I took a look at you data, and made some edits to the wm that help to push out the surfaces to the bottom of the sulci. I attached screenshots of the same slices you sent before, with the original white and pial surfaces in green and blue, and the ones created after editing in yellow and red. Below are some instructions on how to make these edits. First, select the wm volume and change the color map to Heat on the panel on the lower left. Set the opacity to ~0.15-0.25 so you can see the brainmask behind it. Then, lower the Mid to zero (where my pointer is in wm_edit_1.png; you can keep the other values at their defaults). By doing this, everything that you erase using Recon Edit will show up in red so that it is easy to see. Next, erase a line at the start of the sulcus where you want to push out the surface (wm_edit_2.png), then select the fill tool and hold shift and click inside the sulcus to erase the whole section (wm_edit_3.png). Do this for a few slices around each location that needs to be pushed out so that it has more effect, then save the wm volume and rerun recon-all. Hope this helps, and let me know if you have any more questions. Best, Lee On Wed, 21 Jan 2015, Celine Louapre wrote: Hi everyone I don't know if someone had the chance to look at the data we uploaded for advice to edit the recons (see below). Thank you so much Celine On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: Thanks Bruce The aseg is correct, no ventricule labeled there (I was used to that) that I could see. I couldn't find the topological defect indeed, and what is strange if that the wrong surface on the right hemisphere were correct after autorecon2 but incorrect after autorecon3. The problem on the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 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 mailing list 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.
Re: [Freesurfer] Problem with a recon edit
Hi everyone I don't know if someone had the chance to look at the data we uploaded for advice to edit the recons (see below). Thank you so much Celine On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: Thanks Bruce The aseg is correct, no ventricule labeled there (I was used to that) that I could see. I couldn't find the topological defect indeed, and what is strange if that the wrong surface on the right hemisphere were correct after autorecon2 but incorrect after autorecon3. The problem on the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 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 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] Problem with a recon edit
Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Problem with a recon edit
Thanks Bruce The aseg is correct, no ventricule labeled there (I was used to that) that I could see. I couldn't find the topological defect indeed, and what is strange if that the wrong surface on the right hemisphere were correct after autorecon2 but incorrect after autorecon3. The problem on the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 mailing list 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.
Re: [Freesurfer] Scatter plot from mri_glmfit analyses
Thanks, indeed we used --pvr.
The command line was:
mri_glmfit \
--y ${PATH_DIR}/{surf}.mgh \
--pvr CT_surf.mgh \
--fsgd myfsgd.fsgd \
--C cont.mat \
--surf fsaverage $hemi \
--glmdir outputdir \
--mask mask_minimum_of_subjects.mgh \
--frame-mask mask_for_0_values.mgh \
--no-prune
Would there be a way to work around, or should I just try to do it only
from non pvr glm analyses?
Celine
X and C have different numbers of columns. What was your mri_glmfit
command line? If you used a --pvr, then the pcc script will not work.
doug
On 09/22/2014 01:21 PM, Celine Louapre wrote:
Thanks for pointing me to the file and the help. I found the info I
needed
there fro the cache.th13.abs.y.ocn.dat file.
For the partial correlation coefficient script fast_glm_pcc.m I could
not
make it run however. I got this error:
Error using *
Inner matrix dimensions must agree.
Error in fast_glm_pcc (line 28)
Xc = X*C';
And also I found this info in the script WARNING: X must have a column
of
1s or both X and y must have been demeaned before the glm.
But I am not sure about what it means. Attached are Xg.dat and C.dat
files.
Thanks again for your help
Celine
should be something like cache.th13.abs.y.ocn.dat
also, you can look in mri_glmfit-sim --help to get info about each
output file
On 09/19/2014 04:47 PM, Celine Louapre wrote:
Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat?
The cache.th13.abs.sig.ocn.annot contains the significant clusters it
that
correct? So to get individual mean values from cluster 1 for example
where
should I look?
Thanks!
Celine
Have you run mri_glmfit-sim? It will create labels (ie, annotations)
of
the clusters as well as run mri_segstats to get means in each cluster
for each subject. Try that link now
doug
On 09/18/2014 12:15 PM, Celine Louapre wrote:
Hi Doug and FS team
I did glm analyses using mri_glmfit, and I was trying to plot the
individual values in the population for a specific significant
cluster.
However I am not sure how to extract individual values from the
entire
cluster. (note that the concatenated surface used as input for the
glm
contains some 0 values that I want to exclude from the mean value of
the
cluster).
Is there a way to build a label from a specific significant cluster?
Then, I was thinking about using mri_segstats --avgwf on the 4D
concatenated file to get the average of the region but is there a
way
to
not include 0 values?
And then I was also interested in getting the correlation
coefficient
from
that same cluster, so maybe the script below would be helpful for
that
but
I could not open it.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m
Thanks so much for your help
Best
Celine
On 05/31/2012 06:09 AM, Knut J Bjuland wrote:
Hi
I am trying to calculate correlation coefficient using freesurfer
GLM
for associations between volumes and IQ. I found this ealier
answar,
but the matlab script but the link appear to be dead.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html
Best regards
Knut J
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
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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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing
Re: [Freesurfer] Scatter plot from mri_glmfit analyses
Thanks for pointing me to the file and the help. I found the info I needed there fro the cache.th13.abs.y.ocn.dat file. For the partial correlation coefficient script fast_glm_pcc.m I could not make it run however. I got this error: Error using * Inner matrix dimensions must agree. Error in fast_glm_pcc (line 28) Xc = X*C'; And also I found this info in the script WARNING: X must have a column of 1s or both X and y must have been demeaned before the glm. But I am not sure about what it means. Attached are Xg.dat and C.dat files. Thanks again for your help Celine should be something like cache.th13.abs.y.ocn.dat also, you can look in mri_glmfit-sim --help to get info about each output file On 09/19/2014 04:47 PM, Celine Louapre wrote: Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat? The cache.th13.abs.sig.ocn.annot contains the significant clusters it that correct? So to get individual mean values from cluster 1 for example where should I look? Thanks! Celine Have you run mri_glmfit-sim? It will create labels (ie, annotations) of the clusters as well as run mri_segstats to get means in each cluster for each subject. Try that link now doug On 09/18/2014 12:15 PM, Celine Louapre wrote: Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Xg.dat Description: Binary data C.dat Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] Scatter plot from mri_glmfit analyses
Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat? The cache.th13.abs.sig.ocn.annot contains the significant clusters it that correct? So to get individual mean values from cluster 1 for example where should I look? Thanks! Celine Have you run mri_glmfit-sim? It will create labels (ie, annotations) of the clusters as well as run mri_segstats to get means in each cluster for each subject. Try that link now doug On 09/18/2014 12:15 PM, Celine Louapre wrote: Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] Scatter plot from mri_glmfit analyses
Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J ___ 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 gr...@nmr.mgh.harvard.edu 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 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.
Re: [Freesurfer] select_talairach_point function?
Hi I just find out how to launch the command, it is in the terminal where tksurfer is running, after the % sign. (I didn't understand what the tcl window was meaning) Best Celine Hi I am sorry if my question is really basic, but I am choosing the seeds for fsfast resting state connectivity analysis, and I am looking at the different options in the litterature. Seeds are often presented with the talairach coordinates, and I was looking for a way to find the corresponding vertex number on fsaverage surface, so that I can build the corresponding label that I could use for the fcseed-sess command. I found this previous email, and there seem to be a command to do that but I don't know how to launch this command select_talairach_point xtal ytal ztal Thank you very much Celine -Message d'origine- De : Bruce Fischl [mailto:fischl at nmr.mgh.harvard.edu] Envoyé : mercredi, 10. février 2010 16:18 À : Ben Hamida Cammoun Leila Faiza Cc : freesurfer at nmr.mgh.harvard.edu Objet : Re: [Freesurfer] ROI based on Talairach coordinate Hi Leila, you can use the tcl command select_talairach_point xtal ytal ztal in tksurfer in the tcl window (with the % prompt), then make a label from that point and dilate it a few times. cheers, Bruce On Wed, 10 Feb 2010, Ben Hamida Cammoun Leila Faiza wrote: Dear Freesurfer users and experts, This is my second attempt :( I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. My first try was to use the transformation Talairach.xfm with matlab, inverse it and try to recover RAS coordinate, it gives me completely wrong values. Second try was to introduce the Tal coordinate directly in Tksurfer, which is not possible I think (correct me if I am wrong), with the version I have the is a bug in tkmedit I guess when introducing Talairach coord (the ideas was to save them and to load the vertex in tksurfer).. the values changes in the edit box.. Is there another way?? Is it possible with script? Or how to do this by matlab? Please don't ignore the request. Leila ___ 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 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] select_talairach_point function?
Hi I am sorry if my question is really basic, but I am choosing the seeds for fsfast resting state connectivity analysis, and I am looking at the different options in the litterature. Seeds are often presented with the talairach coordinates, and I was looking for a way to find the corresponding vertex number on fsaverage surface, so that I can build the corresponding label that I could use for the fcseed-sess command. I found this previous email, and there seem to be a command to do that but I don't know how to launch this command select_talairach_point xtal ytal ztal Thank you very much Celine -Message d'origine- De : Bruce Fischl [mailto:fischl at nmr.mgh.harvard.edu] Envoyé : mercredi, 10. février 2010 16:18 À : Ben Hamida Cammoun Leila Faiza Cc : freesurfer at nmr.mgh.harvard.edu Objet : Re: [Freesurfer] ROI based on Talairach coordinate Hi Leila, you can use the tcl command select_talairach_point xtal ytal ztal in tksurfer in the tcl window (with the % prompt), then make a label from that point and dilate it a few times. cheers, Bruce On Wed, 10 Feb 2010, Ben Hamida Cammoun Leila Faiza wrote: Dear Freesurfer users and experts, This is my second attempt :( I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. My first try was to use the transformation Talairach.xfm with matlab, inverse it and try to recover RAS coordinate, it gives me completely wrong values. Second try was to introduce the Tal coordinate directly in Tksurfer, which is not possible I think (correct me if I am wrong), with the version I have the is a bug in tkmedit I guess when introducing Talairach coord (the ideas was to save them and to load the vertex in tksurfer).. the values changes in the edit box.. Is there another way?? Is it possible with script? Or how to do this by matlab? Please don't ignore the request. Leila ___ Freesurfer mailing list 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] Extract seed from resting state networks mask (Yeo and Buckner maps)
Hi Freesurfer team
I am running a functional connectivity analysis on resting state data, and
I would like to use as seed the precuneus/posterior cingulate region as
seen on fsaverage/label/${hemi}.Yeo2011_17Networks_N1000.annot.
However, this region is part of the label 17Networks_16 comprising other
regions. Is it possible to isolate this specific portion of the label to
create a seed region for the connectivity analysis ? I tried to do it on
tksurfer, drawing a path around the region but then I could not figure out
how to extract this part of the label.
Thank you very much for your help
Best
Celine
--
Celine Louapre, MD-PhD
Research Fellow at Massachusetts General Hospital
Department of Radiology, MGH
Building 149, Room 2301
13th Street
Charlestown, MA 02129
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Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
oh yes I see, I have renamed the dpath/${TRACT[$num_tract]} directories to
have a backup, so the name is not correct anymore. Actually I didn't need
to do that, I can just set a different name for the outputs
pathpathstats.byvoxel.txt and pathstats.overall.txt
Thanks
Celine
Hi Celine - This command assumes that --intrc is a tracula output
directory, containing all the files that tracula saves in such a
directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
Hi Anastasia
I have finally managed to coregister and resample all lesion masks on
DTI
images :-), and as you suggested I set the lesion voxels to 0 in
dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below
(where TRACT is the full name of the tract and SHORT_TRACT is the short
name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase
${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path
${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt
--outvox
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how
to
set the output type
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: must specify at least one type of output
Would you have some idea about that?
Thank you very much
Celine
Hi Celine - That's an interesting question. There's nothing implemented
in
there right now that would allow you to skip part of the tract in the
along-the-tract stats. One (not very elegant) way to try to do
something
like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for
backup
first.) If you want the same for the diffusivities, repeat for the also
for the MD, L1, L2, L3 volumes.
2. Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of
the
tract that go through the lesions will have zero values (or very low,
if
they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement
something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts,
I am trying to get DTI values along the tracts as in the
pathstatbyvoxel
file, but excluding inflammatory WM lesions. I have masks of the WM
lesions that I could apply on the DTI maps, but then how could I
compute
the DTI metrics along the tract with the exclusion of the lesion? (I
guess
the last step of trac-all -path could be applied to DTI maps that were
masked by the lesions?)
I would like to keep the advantage of having the DTI weighted metrics
in
particular.
Thanks a lot for your help!
Celine
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Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
Hi Anastasia
I have finally managed to coregister and resample all lesion masks on DTI
images :-), and as you suggested I set the lesion voxels to 0 in
dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below
(where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase
${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path
${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt
--outvox
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to
set the output type
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: must specify at least one type of output
Would you have some idea about that?
Thank you very much
Celine
Hi Celine - That's an interesting question. There's nothing implemented in
there right now that would allow you to skip part of the tract in the
along-the-tract stats. One (not very elegant) way to try to do something
like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup
first.) If you want the same for the diffusivities, repeat for the also
for the MD, L1, L2, L3 volumes.
2. Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the
tract that go through the lesions will have zero values (or very low, if
they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts,
I am trying to get DTI values along the tracts as in the pathstatbyvoxel
file, but excluding inflammatory WM lesions. I have masks of the WM
lesions that I could apply on the DTI maps, but then how could I compute
the DTI metrics along the tract with the exclusion of the lesion? (I
guess
the last step of trac-all -path could be applied to DTI maps that were
masked by the lesions?)
I would like to keep the advantage of having the DTI weighted metrics in
particular.
Thanks a lot for your help!
Celine
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Re: [Freesurfer] Pb with a registration of diffusion images processed with tracula and anat images
Thnak you very much for clarifying this. So recon-all and trac-all outputs are all in their own native space. Now if I need to sample surfaces on the diffusion images based on recons surface, I need to provide the /dmri/xfms/anatorig2diff registration matrix right? But it is not completely clear to me if anatorig2diff is the registration matrix from the anat to the diffusion space or the opposite? Because when I am loading brainmask from recon-all, then loading lowb.nii.gz using the anatorig2diff registration file, the registration is fine (and especially now that I have targeted a subject from whom the 2 spaces are really different, it is easier to figure out about registration). So anatorig2diff means diffusion space to anat space? Thanks a lot Celine I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from recon-all, they will be in their respective native spaces, and thus I wouldn't expect them to be registered to each other. On the other hand, any brain masks that trac-all saves under dlabel/diff/ are in diffusion space, so those can be viewed with lowb.nii.gz without a registration file. On Fri, 28 Feb 2014, Douglas N Greve wrote: In general you should use a registration file when viewing your results. In many cases, it may look like it is in registration with out a registration file. This can happen if you acquired your anatomical and DTI data in the same session. For this subject, were they acquired in different sessions or was the subject removed and replaced back in the scanner? When you sample the data onto the surfaces, you should always use a registration file. doug On 02/27/2014 05:08 PM, Celine Louapre wrote: Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine ___ 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 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] Pb with a registration of diffusion images processed with tracula and anat images
Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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.
Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
Hi all When you loaded the lowb into freeview and it looked registered with the anatomical, did you load the lowb with the registration file? If not, then the registration may be wrong. Things may look almost right when you don't specify a registration file because you probably collected the dti and anatomical in the same session. If so, then check the registration with something like tkregister2 --mov lowb.nii.gz --reg anatorig2diff.bbr.dat --surfs I did not load it with the registration file, but I just did and it does not change the results on freeview. I also checked the registration on tkregister and it seems very fine to me. also, what is the first value in anatorig2diff.bbr.dat.mincost? Here are all the values: 0.180949 209.653007 285.934948 29.944402 Maybe one point that I don't understand is why we have to apply a registration matrix if all the volumes (brainmask.mgz, lowb.nii.gz and the lesion mask) are already registered? Because if I am applying the invert of registration matrix anatorig2diff.bbr.dat to the lesion mask, then it will be in the native diffusion space, not the recons space anymore, isn't it? doug On 2/17/14 10:41 PM, Celine Louapre wrote: The lesion_vol2vol volume is still not correctly overlapping the DTI. The only command that didn't give me registration issue is mri_convert where I did not put any registration file but I was not completely happy with the interpolation resampling. (nearest missed some lesions, maybe interpolate and then binarize the mask was one possible option). I can show you the results tomorrow if you prefer Celine what does it look like if you run tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 On 2/17/14 10:00 PM, Celine Louapre wrote: No problem, sorry! So when I am loading my lesion mask on freeview on brainmask.mgz and on DTI_fit_FA.nii, the lesions are correctly registered on both DTI and T1. The only thing I would like to do is to resample the lesion mask that has a resolution of 0.3*0.3*1 on the resolution of the DTI that has 1.8mm^3. When I am using the command below with mri_vol2vol, and the registration matrix anatorig2diff.bbr.dat, the output is a lesion mask that has 1.8mm3 resolution, but the lesions are not overlapping the other modalities and the previous mask on freeview. Is it the way I am loading it on freeview maybe? or actually all the volumes are already on the recons space so maybe I should not use any registration matrix? Celine oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: Hi Doug I don't know if you had the chance to read my email below to resample a lesion mask on diffusion images. Anastasia gave me the registration file to use (anatorig2diff.bbr.dat) in the command but the output mask file was not registered anymore. So she asked me to rephrase my question more generally on the mailing list to look for help with bbregister. Thanks a lot Celine Original Message Subject: [Freesurfer] Resample a mask on diffusion images using bbregister registration matrix From:Celine Louapre cel...@nmr.mgh.harvard.edu Date:Thu, February 13, 2014 9:58 pm To: freesurfer@nmr.mgh.harvard.edu -- Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot
Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
No problem, sorry! So when I am loading my lesion mask on freeview on brainmask.mgz and on DTI_fit_FA.nii, the lesions are correctly registered on both DTI and T1. The only thing I would like to do is to resample the lesion mask that has a resolution of 0.3*0.3*1 on the resolution of the DTI that has 1.8mm^3. When I am using the command below with mri_vol2vol, and the registration matrix anatorig2diff.bbr.dat, the output is a lesion mask that has 1.8mm3 resolution, but the lesions are not overlapping the other modalities and the previous mask on freeview. Is it the way I am loading it on freeview maybe? or actually all the volumes are already on the recons space so maybe I should not use any registration matrix? Celine oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: Hi Doug I don't know if you had the chance to read my email below to resample a lesion mask on diffusion images. Anastasia gave me the registration file to use (anatorig2diff.bbr.dat) in the command but the output mask file was not registered anymore. So she asked me to rephrase my question more generally on the mailing list to look for help with bbregister. Thanks a lot Celine Original Message Subject: [Freesurfer] Resample a mask on diffusion images using bbregister registration matrix From:Celine Louapre cel...@nmr.mgh.harvard.edu Date:Thu, February 13, 2014 9:58 pm To: freesurfer@nmr.mgh.harvard.edu -- Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine ___ Freesurfer mailing list 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.
Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
The lesion_vol2vol volume is still not correctly overlapping the DTI. The only command that didn't give me registration issue is mri_convert where I did not put any registration file but I was not completely happy with the interpolation resampling. (nearest missed some lesions, maybe interpolate and then binarize the mask was one possible option). I can show you the results tomorrow if you prefer Celine what does it look like if you run tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 On 2/17/14 10:00 PM, Celine Louapre wrote: No problem, sorry! So when I am loading my lesion mask on freeview on brainmask.mgz and on DTI_fit_FA.nii, the lesions are correctly registered on both DTI and T1. The only thing I would like to do is to resample the lesion mask that has a resolution of 0.3*0.3*1 on the resolution of the DTI that has 1.8mm^3. When I am using the command below with mri_vol2vol, and the registration matrix anatorig2diff.bbr.dat, the output is a lesion mask that has 1.8mm3 resolution, but the lesions are not overlapping the other modalities and the previous mask on freeview. Is it the way I am loading it on freeview maybe? or actually all the volumes are already on the recons space so maybe I should not use any registration matrix? Celine oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: Hi Doug I don't know if you had the chance to read my email below to resample a lesion mask on diffusion images. Anastasia gave me the registration file to use (anatorig2diff.bbr.dat) in the command but the output mask file was not registered anymore. So she asked me to rephrase my question more generally on the mailing list to look for help with bbregister. Thanks a lot Celine Original Message Subject: [Freesurfer] Resample a mask on diffusion images using bbregister registration matrix From:Celine Louapre cel...@nmr.mgh.harvard.edu Date:Thu, February 13, 2014 9:58 pm To: freesurfer@nmr.mgh.harvard.edu -- Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine ___ Freesurfer mailing list 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] resample lesion mask on diffusion images processed with tracula
Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case? I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use. And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space? Thanks a lot in advance for your help Best Celine ___ Freesurfer mailing list 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.
Re: [Freesurfer] resample lesion mask on diffusion images processed with tracula
Hi Anastasia Thanks for your answer. I think I am missing something because I tried with this registration file but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seemed correctly registered on both. the command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel sieze is the same as the DTI images, but the lesions are not at the same place. That is why I thought I had picked the wrong registration file...? Celine Hi Celine - If the lesion mask is already in the space of the freesurfer recon, you can pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat transform. That's the one generated by bbregister for the anatomical-diffusion registration. Hope this helps, a.y On Thu, 13 Feb 2014, Celine Louapre wrote: Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case? I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use. And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space? Thanks a lot in advance for your help Best Celine ___ 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 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] Resample a mask on diffusion images using bbregister registration matrix
Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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.
Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula
Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 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] Compute DTI metrics in NAWM in Tracula
Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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] GLM p value display
Hi all I am wondering what is the best to present GLM results in a table on top of the visual display. For the significant clusters after clusterwise correction, should we display the Max -log10(p) as in the summary file itself, or the p value directly, or a transformed pvalue like a Z score? Thanks for advices Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list 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.
Re: [Freesurfer] GLM p value display
Oh so we don't report the significance itself? because for example if we have a small cluster but highly significant, does the cluster-wise correction p value take it into account? (compared to a large cluster but with lower significance). I may not have completely got this. Thanks Doug Celine Hi Celine, you should report the clusterwise p-value (which is neither of those). doug On 12/17/2013 12:11 PM, Celine Louapre wrote: Hi all I am wondering what is the best to present GLM results in a table on top of the visual display. For the significant clusters after clusterwise correction, should we display the Max -log10(p) as in the summary file itself, or the p value directly, or a transformed pvalue like a Z score? Thanks for advices Celine -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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.
