Re: [Freesurfer] within-subject contrast between runs
External Email - Use Caution Dear Mr. Greve Thanks for your suggestions. However I'm still a bit puzzled about how to contrast two runs corresponding to different stimulations (StimA: runA and StimB:runB) from one subject. I have two runs each containing a paradigm file corresponding to one of the two stimulations. How is it possible to contrast those two stimulation conditions acquired in two different runs since one run and thus also the paradigm file does not contain both stimulation conditions? Seemingly both stimulation conditions must be in one paradigm file set to different onset timings to perform mkcontrast-sess My folder Structure is as follows Project Name Session = Subject Runs (001, 002) = Stimulation A and Stimulation B, each with a separate paradigm file I know that I do not have to model the no-stimulation periods explicitely Best wishes Chris Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve Gesendet: Freitag, 6. März 2020 17:54:16 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] within-subject contrast between runs On 3/6/2020 11:15 AM, Milde, Christopher wrote: External Email - Use Caution Dear Freesurfer Experts, I have a very basic questions about creating subject-wise contrasts between runs Background Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off). I performed the preprocessing and 1st levels stats in the native subjects space Questions * How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session? The easiest way is to code the conditions differently in the paradigm file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just create contrasts as normal * Can I obtain this within-subject contrast by staying in the native subject space? It can be done in fsaverage or the native subject surface space, it is not related. * Do I have to concatenate both runs and create a new parradigm file? No, see above Thanks for your support Sincerely Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] within-subject contrast between runs
External Email - Use Caution Dear Freesurfer Experts, I have a very basic questions about creating subject-wise contrasts between runs Background Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off). I performed the preprocessing and 1st levels stats in the native subjects space Questions * How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session? * Can I obtain this within-subject contrast by staying in the native subject space? * Do I have to concatenate both runs and create a new parradigm file? Thanks for your support Sincerely Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Definition of circular label centered on peak vertex
External Email - Use Caution Dear FS experts I`m interested in extracting beta values from a FSFAST analysis performed in the subject`s native space. The beta values shall be extracted from a circular label around the peak vertex. How can you define a circular label centered on the peak to extract average stats (e.g. betas) from that label? I`m aware how to create mask from the whole clusters in a given ROI saving them as labels and extracting stats. However I`m not sure how to define a circular mask or label. Thanks in advance Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] epidewarp.fsl radian phase range error
Dear FS experts, I also encountered this problem when trying to apply epidewarp.fsl: ERROR: input phase image exceeds allowable phase range. Allowable range is 6.283 radians. Image range is: 12.5633 radians I read that there is an updated version of epidewarp.fsl which might solve this problem. Can I rescale the phase images? I appreciated any support. Best, 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.
[Freesurfer] interhemispheric registration in native space
Dear Freesurfer experts, is there a way to perform an interhemispheric registration with rh, lh surfaces in native space? Preferentially, I would perform the registration with smoothwm surfaces. I only found the xhemi command which refers to fsaverage as a target Best wishes, 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
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
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
[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)
Dear FS experts I extracted the vertex indices of several subjects. But unfortunately I did not extract the corresponding Vertex RAS values. Is there a command to translate the Vertex Index into a Vertex RAS so that I do not have to scroll through all the subjects again? I would like to script the translation from Vertex Index to Vertex RAS Best wishes, 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.
[Freesurfer] computing cluster overlap
Dear Freesurfer-Experts, I'm looking for an elegant way of computing degree of overlap between activated clusters within-subject and between sessions (transversal) on the smoothwm. I thought about running a conjunction analysis between the sessions to detect the extents of common activations, but maybe there are much better ways? I'm thankful for any advice, Best wishes, 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.
[Freesurfer] missing files in fsaverage folder
Dear Freesurfer Experts, is there an easy way to update only folders within the Freesurfer folder? Accidentally, I deleted the fsaverage folder from the Freesurfer version. I copied the fsaverage folder from another Freesurfer installation. But seemingly some essential files (e.g. perirhinal label) are missing because of different FS versions. Due to some missing files in fsaverage some commands do not run. Furthermore, I cannot find some tools like stxgrinder-sess or func2roi-sess within the FSFAST package. So, is there an easy way to make an update? Info: I’m using Freesurfer v5.3.0 for Linux-centos4 I’m thankful for any advice, Cheers, Chris ___ 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] multiple comparisons correction for individual hemispheres (native space)
Dear Doug, Unfortunately, it doesn't make a difference if I'm using a dot or comma or simply type in 2 or 3 as a threshold. The terminal output always shows me the converted version with a comma 2.3 -- 2,3 or 2 -- 2,0 which is not recognized by the command. Maybe I have to change the default settings of floats in the bash using printf? Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Mittwoch, 10. Dezember 2014 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: Dear Doug, I tried to run MCC with cluster-sess but unfortunately I got the same error message like when I'm using mri_glmfit-sim. It does not recognize the thresh (cluster-forming thresh) Here is the terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/christopher/Desktop/freesurfer FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects MNI_DIR /home/christopher/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1 [christopher@fu20a S1]$ cd $proj_dir [christopher@fu20a S1]$ [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Montag, 24. November 2014 20:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, 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 -- 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
Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)
Dear Doug, I tried to run MCC with cluster-sess but unfortunately I got the same error message like when I'm using mri_glmfit-sim. It does not recognize the thresh (cluster-forming thresh) Here is the terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/christopher/Desktop/freesurfer FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects MNI_DIR /home/christopher/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1 [christopher@fu20a S1]$ cd $proj_dir [christopher@fu20a S1]$ [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Montag, 24. November 2014 20:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, 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
[Freesurfer] multiple comparisons compensation for first-level analysis
Dear Freesurfer experts, I'm not sure how to apply cluster-wise correction for multiple comparisons when one is not interested in doing group statistics. For group analysis you concatenate individuals into one file and use mri_glmfit and mri_glmfit-sim to run general linear model and simulations. I want to apply multiple comparisons only within the individual subjects (stay at first-level), so that I don't have glm directories created by mri_glmfit. I ran recon-all with -qcache, so I have pre-computed MC simulations. I used the -fwhm option during selxavg3-sess to estimate smoothness. è pre-cached simulation I have fMRI-data. Do you have any suggestions? Sincerely yours, 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.
[Freesurfer] multiple comparisons correction for individual hemispheres (native space)
Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, 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.
[Freesurfer] mkanalysis-sess blocked design
Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for condition and fixation? I'm using Freesurfer 5.3 Thanks in advance, Chris ___ 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] mkanalysis-sess blocked design
I solved the problem. I figured out that the event-related flag also refers to blocked-designs Best wishes Chris Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Milde, Christopher Gesendet: Mittwoch, 3. September 2014 14:12 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] mkanalysis-sess blocked design Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for condition and fixation? I'm using Freesurfer 5.3 Thanks in advance, Chris ___ 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] 3dvolreg.afni error during mc-sess
Dear Doug, Finally, I was able to solve the 3dvolreg.afni error problem. I installed the recent AFNI version for Linux and replaced the 3dvolreg file in Freesurfer/bin by the AFNI 3dvolreg.afni of the AFNI software package. After adding the Suffix .afni (the AFNI-3dvolreg file doesn't end with .afni) the mc-sess runs well. Best wishes, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Freitag, 22. August 2014 18:42 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] 3dvolreg.afni error during mc-sess Hmm, that means that 3dvolreg.afni that comes with FS does not run properly on your system. Do you already have a full version of AFNI installed on your system? doug On 08/22/2014 05:00 AM, Milde, Christopher wrote: Dear Freesurfer Experts, I'm struggling with running only motion correction. After running mktemplate-sess which ran well, the mc-sess terminates with the following error. The terminal otput is attached: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Some important comments: 1.) 3dvolreg.afni is within the bin-folder of Freesurfer 2.) I use partial-field-of-view EPI 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a prerequisite to use unpacksdcmdir)? Thank you, for your support!!! Greets Christopher *TERMINAL OUTPUT:* mc-sess -s PM_00031 -d $FSF_DIR -per-run -fstem -outfmt nii.gz [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 -outfmt nii.gz fmt: Undefinierte Variable. [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 Logfile is /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold. log --- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923 RunList: 001 002 004 --- ** --- --- Motion Correcting Run 001 --- --- ** --- sess = PM_00923 Fr 22. Aug 09:35:07 CEST 2014 mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz log file is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is 001/tmp.mc-afni2.19767 #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/tempvol.nii.gz... #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/20.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/invol.nii.gz... #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix 001/tmp.mc-afni2.19767/outvol.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Ungültiger leerer Befehl. ___ 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
[Freesurfer] 3dvolreg.afni error during mc-sess
Dear Freesurfer Experts, I'm struggling with running only motion correction. After running mktemplate-sess which ran well, the mc-sess terminates with the following error. The terminal otput is attached: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Some important comments: 1.) 3dvolreg.afni is within the bin-folder of Freesurfer 2.) I use partial-field-of-view EPI 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a prerequisite to use unpacksdcmdir)? Thank you, for your support!!! Greets Christopher TERMINAL OUTPUT: mc-sess -s PM_00031 -d $FSF_DIR -per-run -fstem -outfmt nii.gz [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 -outfmt nii.gz fmt: Undefinierte Variable. [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 Logfile is /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold.log --- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923 RunList: 001 002 004 --- ** --- --- Motion Correcting Run 001 --- --- ** --- sess = PM_00923 Fr 22. Aug 09:35:07 CEST 2014 mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz log file is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is 001/tmp.mc-afni2.19767 #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/tempvol.nii.gz... #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/20.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/invol.nii.gz... #@# /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix 001/tmp.mc-afni2.19767/outvol.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Ungültiger leerer Befehl. ___ 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_surfcluster for FEAT cluster maxima
Dear Doug, thanks for your helpful comments according to the reading out fMRI cluster peak vertices! Actually, I'm able now to read out cluster peak vertices (see bottom). I applied the mri_surfcluster command for resampled and surface smoothed Feat stats on smoothwm surface with projfrac 0.5 (mri_surf2surf -fwhm). But I'm not sure how to apply Multiple Comparison Correction because I only found this option for group statistics (mri_glmfit-sim). For this purpose, I have to generate a GLM within Freesurfer. I use FEAT preprocessed but unsmoothed data and coregistered/resampled it to the surfaces. My goal is to read out peak vertices on session/single-subject level, preferentially on the smoothwm with -projfrac 0.5. Is it possible to use the mkanalysis-sess/mkcontrast-sess/selxvavg3-sess commands (seemingly it’s just for FSFAST preprocessed data) in combination with a Multiple Comparisons Correction at session level? OR Shall I run the Preprocessing in FSFAST too? Hopefully, there is a solution for this delicate problem Sincerely yours, Chris mri_surfcluster --subject PM_00880_inflation --surf smoothwm --hemi lh --in PM_00880_inflation/TR.feat/stats/smooth_10.mgz --thmin 2 --thmax inf --sign pos --minarea 30 --annot aparc --sum PM_00880_inflation/TR.feat/stats/TR_summary2 thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = PM_00880_inflation/TR.feat/stats/smooth_10.mgz srcsubjid = PM_00880_inflation srcsurf= smoothwm srcframe = 0 thsign = pos thmin = 2 thmax = inf fdr= -1 minarea= 30 xfmfile= talairach.xfm nth = -1 sumfile = PM_00880_inflation/TR.feat/stats/TR_summary2 subjectsdir= /home/christopher/Desktop/freesurfer/subjects FixMNI = 1 - XFM matrix (RAS2RAS) --- /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/mri/transforms/talairach.xfm 1.052 0.044 -0.055 0.749; -0.027 1.026 0.319 -8.121; 0.030 -0.345 1.096 -13.593; 0.000 0.000 0.000 1.000; Reading source surface /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/surf/lh.smoothwm Done reading source surface Reading annotation /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 133455 Done loading source values (nvtxs = 133455) overall max = 5.55723 at vertex 63001 overall min = -4.84855 at vertex 19315 surface nvertices 133455 surface area 79513.531250 surface area 79513.859375 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=2.00 (1.698970), thmax=inf (inf), thsignid=1, minarea=30.00 Found 9 clusters Max cluster size 1315.766113 INFO: fixing MNI talairach coordinates ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] mri_surfcluster for FEAT cluster maxima
Dear Freesurfers, I’m struggling with finding a way of getting a table of the cluster maxima of FEAT functional data registered to (reg-feat2anat) and resampled to (feat2surf) reconstructed surfaces. I want to extract cluster maxima for single subjects but preferentially NOT in fsaverage group space. The command mri_surfcluster seems to be quite promising for this purpose. Specifically the summary file with the VtxMax But, seemingly I use the wrong input file (-in) for the FEAT functional data (Error wrong type for mghRead). 1.) Is it at all possible to read resampled Feat data with mri_surfcluster? 2.) is it a prerequisite to run mri_glmfit as suggested in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat (I do not want to perform analysis in group space) I'm very thankful for advice Sincerely yours, Chris $ mri_surfcluster --subject PM_02173_inflation --in PM_02173_inflation/ML_us.feat/stats/zstat1.mgh --hemi lh --surf smoothwm --thmin 2 --thmax inf --sign pos --minarea 15 --annot aparc thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = PM_02173_inflation/ML_us.feat/stats/zstat1.mgh srcsubjid = PM_02173_inflation srcsurf= smoothwm srcframe = 0 thsign = pos thmin = 2 thmax = inf fdr= -1 minarea= 15 xfmfile= talairach.xfm nth = -1 subjectsdir= /home/christopher/Desktop/freesurfer/subjects FixMNI = 1 - XFM matrix (RAS2RAS) --- /home/christopher/Desktop/freesurfer/subjects/PM_02173_inflation/mri/transforms/talairach.xfm 1.127 -0.010 -0.020 0.954; 0.005 0.993 0.048 -16.639; 0.017 -0.052 1.162 -15.969; 0.000 0.000 0.000 1.000; Reading source surface /home/christopher/Desktop/freesurfer/subjects/PM_02173_inflation/surf/lh.smoothwm Done reading source surface Reading annotation /home/christopher/Desktop/freesurfer/subjects/PM_02173_inflation/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values mghRead(PM_02173_inflation/ML_us.feat/stats/zstat1.mgh, -1): could not open file ERROR: could not read PM_02173_inflation/ML_us.feat/stats/zstat1.mgh as type ___ 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] smoothing functional data on smoothwm surface
Dear Doug, unfortunately, I don't know how to define the source (EPI) and target (smoothwm) within the mri_surf2surf command to apply smoothing on the FEAT functional data. My aim is to apply smoothing of the FEAT functional data AFTER being resampled to the smoothwm (to avoid deficient smoothing due to attached cortical banks given by VBR-approaches) mri_surf2surf --s PM_02173 --hemi lh --sval ??? --fwhm 10 --trgsurfval smoothwm is smooth-out a better option? --smooth-out (to apply smoothing after resampling to the smoothwm) ps: Might tksurfer be an alternative? Using: tksurfer subject lh smoothwm -overlay [FEAT functional] -overlay-reg [...anat2exf.register.dat ] and apply smoothing by using Tools-- Surface -- Overlay Smoothing? Kindly regards, Christopher Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Montag, 16. Juni 2014 17:30 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] smoothing functional data on smoothwm surface Use mri_surf2surf with the --fwhm option doug On 6/16/14 3:13 PM, Milde, Christopher wrote: Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer from metric distortions (like the inflated OR sphere). I thought about using the smoothwm surface. Questions: Which command can I use for smoothing the feat functional data on the smoothwm AND furthermore, how can I extract the cluster maxima afterwards??? I'm thankful for any helpful comment, Greetz, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] smoothing functional data on smoothwm surface
Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer from metric distortions (like the inflated OR sphere). I thought about using the smoothwm surface. Questions: Which command can I use for smoothing the feat functional data on the smoothwm AND furthermore, how can I extract the cluster maxima afterwards??? I'm thankful for any helpful comment, Greetz, 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.
[Freesurfer] Extract peak voxel (vertex) coordinates from surfaces
Dear Freesurfers, I would be interested in figuring out the peak vertex of clusters based on coregistered functional FEAT data with the reconstructed anatomical surfaces. The FEAT preprocessing was run without smoothing and smoothing was applied after the feat2surf Does anyone know how to obtain the peak coordinate (preferentially on smoothwm surface) ? I need exact vertex indices for running mris_pmake Kindly regards, 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.
[Freesurfer] finding cluster peak vertices
Dear Freesurfers, Is there a way to smooth already preprocessed functional images* (FEAT, FSL), which I coregistered to the reconstructed surfaces (reg feat2anat), on the cortical surface? Furthermore, I would be interested in finding the cluster peak vertex after smoothing the EPI on the reconstructed surface. I know that Hagler et al 2006 talked about a vertex search method to find the maximally activated vertex on the surface. Kindly regards, Christopher *the FEAT preprocessed and 1st level statistics FEATs are not smoothed to avoid blurring across attached gyri ___ 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] distance comparisons across subjects in fsaverage group sphere
Dear Freesurfers, In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make. My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations. Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space? Ps: I know that the distances in spherical space are not Euclidian but still geodesic Best wishes and thanks in advance, Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage:http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 ___ 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] distance comparisons across subjects in fsaverage group sphere
Thanx Bruce, I will try out your suggestion and let you know. I think I will get a good estimate of the degree of metric distortions, because I have a lot of subjects tested ;-) If this will not work, or the distortions are to big, I will make use of the Spline Tool in Freeview manually drawing a line within the cortical ribbon between the peak voxels, whereby benefitting from the reconstructed surface brain with superimposed EPI (with post inflation smoothed EPI data) for visual comparison (to benefit from the SBR versus VBR information, to avoid the problem of guessing if an activated cluster belongs to Gyrus A or B when the Cluster is spread along two attached gyri). Maybe I can also make use of the coordinate transormations RAS --sphere Greetz, Christopher Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Montag, 12. Mai 2014 15:46 An: Freesurfer support list Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere Hi Christopher the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get an idea of how much additional distortion is induced by the registration cheers Bruce On Mon, 12 May 2014, Milde, Christopher wrote: Dear Freesurfers, In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make. My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations. Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space? Ps: I know that the distances in spherical space are not Euclidian but still geodesic Best wishes and thanks in advance, Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage:http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 ___ 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] native or fsaverage spherical space for distance measures?
Dear Freesurfers, according to my research and 'playing-around' with Freesurfer tools on measuring distances between vertices or peak voxels, I'm still unsure about the most adequate way of comparing distances between peak voxels corrected for folding patterns. To my current knowledge, I figured out the following procedures: Goal: comparing cortical distances between peak voxels between subjects of different clinical populations 1.)Manual procedure using Freeview spline tool: using orig.mgz + white and pial surfaces + thresh_zstat images (FSL) è Using Measure tool (spline) to create a smoothed line within the cortical ribbon è Output: absolute cortical distances in [mm] è Problem: topologically remote but geometrically close by peak voxels (maybe avoidable by using the RAS to vertex transformation information of the inflated brain) 2.)Automated procedure: using mris_pmake with start vertex stop vertex coordinates derived from the population averaged sphere coordinate systems (fsaverage sphere) (functional data mapped into common sphere by either feat2surf or mris_preproc) è Output: only relative distance measures, but the comparability between peak voxel distances of different subjects is ensured (due to distance measures within a common spherical coordinate system)*. è Problem: no absolute measure of distances anymore (but this is actually no problem because I'm interested in relative differences in cortical reorganization) - Do you have any suggestions which procedure is preferable?? - *Am I right about the comparability of distance measurements between subjects, when using mris_pmake within a common spherical coordinate space?? I appreciate any helpful comment Sincerely yours, Christopher Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage:http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 ___ 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] combine FEAT data with inflated ANATOMY to measure distances
Dear Doug, I'm very thankful for your helpful comments! I will check the feat2surf script and apply it to map FSL-data in individual and common space (preconditions: existing FEATdir with non-smoothed EPI's and applied reg-feat2anat). I will make use of the -projfrac 0.5 to sample in the middle of the cortical ribbon (to account for drain vessel effects). According to the intended distance measures, relative measures between peak voxels are also fine. So, maybe mris_pmake is still a good option... Greets, Chris Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage:http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 20. März 2014 16:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances 1) Use the feat2surf script 2) I have not used mris_pmake myself. I'm guessing it will *work* on the sphere in that it will return a path, but the distances between vertices have no relationship to anatomy. It might fail on a flat map because it is a patch. doug On 03/20/2014 10:43 AM, Milde, Christopher wrote: Dear Surfers, At moment I'm dealing with a huge dataset, preprocessed (with and without smoothing) and statistically analyzed in FSL FEAT. I used the reg-feat2anat to project functional EPI on inflated MPRAGE (recon-all). Because *I'm interested in measuring Euclidian distances between peak voxels*, I want to project *FEAT EPI-data on cortical flat maps (mris_flatten) or spherical surfaces*. èIs it possible to project FEAT-data on flat_maps? èDoes mris_pmake* works equally fine on different projections of the EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances? *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017 866.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/0178 66.html I'm a quite Surfer-newby. So sorry for that maybe stupid question. Thank you in advance, Christopher *Christopher Milde, M.Sc. Biol.* Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage: http://www.zi-mannheim.de/ http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 ___ 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
[Freesurfer] combine FEAT data with inflated ANATOMY to measure distances
Dear Surfers, At moment I'm dealing with a huge dataset, preprocessed (with and without smoothing) and statistically analyzed in FSL FEAT. I used the reg-feat2anat to project functional EPI on inflated MPRAGE (recon-all). Because I'm interested in measuring Euclidian distances between peak voxels, I want to project FEAT EPI-data on cortical flat maps (mris_flatten) or spherical surfaces. è Is it possible to project FEAT-data on flat_maps? è Does mris_pmake* works equally fine on different projections of the EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances? *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/017866.html I'm a quite Surfer-newby. So sorry for that maybe stupid question... Thank you in advance, Christopher Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.mi...@zi-mannheim.de Homepage:http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230 ___ 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.
