Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion
Basically, I try to create the .mgh files from sig.nii.gz and ces.nii.gz files needed for mri_segstats in ROI-analysis. I run already preprocessing and selxavg3-sess stats to produce the different stats files (sii/ces.nii.gz) The .mgh files show the correct anatomy-space dimension (mri_info: 1x1x1 mm; 256^3, beforehand surface dimension 141526 x 1 x 1) but seem to be corrupted. I tried to visualize the whole hemisphere sig.nii.gz converted into sig.mgh but now activations show up despite of highly significant activations visible in the sig.nii.gz To create .mgh files and run the ROI-analysis, I used the following commands: ### resample ces.nii volume to anatomical space #1 resample ces.nii.gz to anatomy mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/ces.nii.gz --reg $sub/bold/001/register.dof6.dat --fstarg --interp nearest -- o $sub/bold/EX.sm5.lh/EX/ces.lh.mgh #2 resample sig.nii.gz to anatomy mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/001/register.dof6.dat --fstarg --interp nearest --o $sub/bold/EX.sm5.lh/EX/sig.lh.mgh #3 run ROI with an unsigned functional constraint mri-segstats --seg $SUBJECTS_DIR/$sub/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --id 410 -id 407 --i $sub/bold/EX.sm5.lh/EX/ces.lh.mgh --maskthresh 2 --masksign abs The ROI analysis always ends up with zero hrf-amplitudes. I appreciate your support, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 17:18 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion Sorry, can you backup and tell me what you are trying to accomplish? doug On 07/02/2015 10:05 AM, Milde, Christopher wrote: Dear Doug, thanks for the immediate response. Actually I checked the registration with freeview/tkregister2 and print out the quality values which are perfectly fine I did the following fMRI-analysis steps FSFAST 1. Preproc-sess (for smoothwm as well as fsaverage space) -- register.dof6.dat in bold/001 and bold/002 folders 2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level stat files is called EX.sm5.lh) 3. And interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes the sig.nii ces.nii as well as txt.files with the mris_surfcluster output) The main problem is the creation of .mgh files as inputs used for ROI-analysis in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh and ces.mgh (using mri_vol2vol) https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriInd ividual_freeview How to transfer the surface nii.gz files into .mgh files used in volume space? Thanks, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 14:49 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christopher wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz - - - here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from
[Freesurfer] mri_vol2surf nii.gz to .mgh conversion
Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz --- here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 5 Writing to PM_04001/bold/lh.sig.mgh Dim: 126553 1 1 Thanks, Christopher ___ 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] mri_vol2surf nii.gz to .mgh conversion
How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christopher wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz --- here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 5 Writing to PM_04001/bold/lh.sig.mgh Dim: 126553 1 1 Thanks, Christopher ___ 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 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] mri_vol2surf nii.gz to .mgh conversion
Dear Doug, thanks for the immediate response. Actually I checked the registration with freeview/tkregister2 and print out the quality values which are perfectly fine I did the following fMRI-analysis steps FSFAST 1. Preproc-sess (for smoothwm as well as fsaverage space) -- register.dof6.dat in bold/001 and bold/002 folders 2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level stat files is called EX.sm5.lh) 3. And interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes the sig.nii ces.nii as well as txt.files with the mris_surfcluster output) The main problem is the creation of .mgh files as inputs used for ROI-analysis in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh and ces.mgh (using mri_vol2vol) https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview How to transfer the surface nii.gz files into .mgh files used in volume space? Thanks, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 14:49 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christopher wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz -- - here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 5 Writing to PM_04001/bold/lh.sig.mgh Dim: 126553 1 1 -- -- Thanks, Christopher ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion
Sorry, can you backup and tell me what you are trying to accomplish? doug On 07/02/2015 10:05 AM, Milde, Christopher wrote: Dear Doug, thanks for the immediate response. Actually I checked the registration with freeview/tkregister2 and print out the quality values which are perfectly fine I did the following fMRI-analysis steps FSFAST 1. Preproc-sess (for smoothwm as well as fsaverage space) -- register.dof6.dat in bold/001 and bold/002 folders 2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level stat files is called EX.sm5.lh) 3. And interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes the sig.nii ces.nii as well as txt.files with the mris_surfcluster output) The main problem is the creation of .mgh files as inputs used for ROI-analysis in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh and ces.mgh (using mri_vol2vol) https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview How to transfer the surface nii.gz files into .mgh files used in volume space? Thanks, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 14:49 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christopher wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz -- - here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 5 Writing to PM_04001/bold/lh.sig.mgh Dim: 126553 1 1 -- -- Thanks, Christopher ___ 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 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
