[Freesurfer] percent signal change
Dear Doug, I am using the FSL-Freesurfer pipeline, with single subject analysis done in Feat and group analysis done using mri_glmfit. Is there a way I can calculate percent signal change from the group analysis output (or any other method which combines single subject output)? Many thanks, Mariam. Mariam Sood PhD student Department of Psychological Sciences Birkbeck, University of London ___ 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] percent signal change
Dear Doug, Thank you for the reply. I want to use the percent change in signal as a measure of effect size for various regions of interest, so would ideally like an average percent signal change in that ROI. I want it at the group data though. Much appreciate your suggestions. Many thanks, Mariam. On 24 Jul 2015, at 17:37, Douglas Greve wrote: > what kind of percent output do you want? FSL does a global > normalization, effectively computing percent change (actually 10th of > percent change I think). If you want voxel-wise percent, then it is more > difficult. > > On 7/24/15 11:11 AM, Mariam Sood wrote: >> Dear Doug, >> >> I am using the FSL-Freesurfer pipeline, with single subject analysis done in >> Feat and group analysis done using mri_glmfit. Is there a way I can >> calculate percent signal change from the group analysis output (or any other >> method which combines single subject output)? >> >> Many thanks, >> Mariam. >> >> >> Mariam Sood >> PhD student >> Department of Psychological Sciences >> Birkbeck, University of London >> >> >> ___ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] reg-feat2anat problem
Hello, I am running reg-feat2anat and facing some problems. First I ran the command in its default mode using FSL initialisation reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. There is a warning coming up WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option. The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning WARNING:: Flipping Left/Right orientation (as det < 0). Not sure whether this warning is something I should worry about. Much appreciate your help. Many thanks, Mariam. ___ 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] reg-feat2anat problem
Hello Doug, sorry for the delay. But thank you for going through the log and giving me helpful advice. The problems I was having with registration were down to the fact that the anatomical (brain mask) and functional were oriented differently and the flirt command line options (search angle in x,y,z:-90 to +90 degrees) used by reg-feat2anat were insufficient for correcting that. Changing those parameters (searchrx, searchry and searchrz to -180 to 180) fixed my problems and gave me good registration. Many thanks, Mariam. On 4 Feb 2014, at 17:15, Douglas N Greve wrote: > > From the output it looks like the func-anat registration is off, > probably because of the partial FoV is causing the FSL registration used > to init BBR to be off (often happens with a partial FoV). Were the > anatomical and functional acquired at the same time? If so, then you'll > have to bypass reg-feat2anat to create the registration. > > Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std > > doug > > > On 02/02/2014 05:59 PM, Mariam Sood wrote: >> Hello Doug, >> Thank you for your reply. I tried to investigate it further and would be >> grateful for your advice. While the reg-feat2anat registration (default FSL >> option) looks way off, the FEAT generated registration, both >> functional-anatomical and functional-standard look fine. I have used >> brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ >> option selected for functional-standard registration and linear 12DOF for >> registration to standard). This is a partial FOV image and the determinant >> of functional & anatomical have opposite signs. Attached, please find my >> reg-feat2anat log file. >> >> Also from your reply, what I understood is that exf2std.reg.dat is generated >> by FSL routines. Won’t exf2anat registration play any part in this? >> >> I also have a T1-weighted alignment scan acquired with the same orientation >> and slice-block centre as the functional data. Is it possible to make use of >> this to get better registration should other methods fail? >> >> Many thanks, >> Mariam. >> >> >> >> >> >> On 30 Jan 2014, at 17:43, Douglas N Greve wrote: >> >>> The second warning you don't need to worry about. I should change that >>> to not be a warning. reg-feat2anat is only registering the functional >>> and anatomical. If the registration to mni152 does not look good, then >>> that is an FSL issue >>> doug >>> >>> On 01/30/2014 11:06 AM, Mariam Sood wrote: >>>> Hello, >>>> >>>> I am running reg-feat2anat and facing some problems. >>>> >>>> First I ran the command in its default mode using FSL initialisation >>>> /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad >>>> registration. There is a warning coming up >>>> ///WARNING: //initial G-W contrast is negative, but expecting positive./ >>>> / If the mov data has a T1 contrast, re-run with --T1/ >>>> >>>> Next I tried the command using -spm option. The within-subject >>>> registration (anat2exf) looks good, but the registration to the >>>> standard does not look that good, although not as bad as with -fsl >>>> option. >>>> >>>> The structural and the functional are using different conventions >>>> (structural is in radiological convention, whereas functional is >>>> neurological). I presume the determinants are associated with this and >>>> they have opposite signs. The orientations are also different. >>>> Additionally in both the log files (one with -fsl option and -spm >>>> option), I get another warning /WARNING:: Flipping Left/Right >>>> orientation (as det < 0). /Not sure whether this warning is something >>>> I should worry about. >>>> >>>> Much appreciate your help. >>>> >>>> Many thanks, >>>> Mariam. >>>> >>>> >>>> >>>> >>>> ___ >>>> 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 >>> FileDr
[Freesurfer] FWHM in mri_glmfit-sim
Hi Doug, I have a few queries regarding FWHM used in multiple comparisons correction program mri_glmfit-sim My data at present is analysed in FSL & Freesurfer following the procedure in the link http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer. No volume based smoothing at single subject level (in FSL) is done at the moment, and a 4 mm surface level smoothing was applied during mris_preproc stage. 1. I have noticed that mri_glmfit computed a FWHM of 8.578114 using residuals. How exactly is this value computed? 2. I understand that the cached simulation used in mri_glmfit-sim is selected based on the above computed smoothness value. Is this fine, or should I override? If I also smooth the data at the single subject level on the volume (in FSL), can I still follow the above process? Many thanks, Mariam. ___ 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] FWHM in mri_glmfit-sim
Hi Doug, Thank you for your advice. Would you also have any advice on what would be the correct process to follow if volume based smoothing at subject level(4mm) and surface based smoothing at group level(4mm) are applied? Many thanks, Mariam. On 31 Mar 2014, at 16:36, Douglas N Greve wrote: > > On 03/31/2014 10:05 AM, Mariam Sood wrote: >> Hi Doug, >> >> I have a few queries regarding FWHM used in multiple comparisons correction >> program mri_glmfit-sim >> >> My data at present is analysed in FSL & Freesurfer following the procedure >> in the link >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer. No >> volume based smoothing at single subject level (in FSL) is done at the >> moment, and a 4 mm surface level smoothing was applied during mris_preproc >> stage. >> >> 1. I have noticed that mri_glmfit computed a FWHM of 8.578114 using >> residuals. How exactly is this value computed? > It is based on the correlation coefficient of the residuals of adjacent > vertices. >> 2. I understand that the cached simulation used in mri_glmfit-sim is >> selected based on the above computed smoothness value. Is this fine, or >> should I override? If I also smooth the data at the single subject level on >> the volume (in FSL), can I still follow the above process? > Do you mean over-ride because you smoothed at 4 but get 8.5? No, you > would use the 8.5. If you smoothed in the volume, depending on how much, > it is probably ok to continue the process (though technically not correct) > doug >> >> Many thanks, >> Mariam. >> >> >> >> >> >> >> >> >> >> ___ >> 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] FWHM in mri_glmfit-sim
Thanks very much Doug. Mariam. On 1 Apr 2014, at 17:17, Douglas N Greve wrote: > > If I could not reanalyze the data, I would just follow the standard process. > doug > > On 04/01/2014 04:12 AM, Mariam Sood wrote: >> Hi Doug, >> Thank you for your advice. Would you also have any advice on what would be >> the correct process to follow if volume based smoothing at subject >> level(4mm) and surface based smoothing at group level(4mm) are applied? >> Many thanks, >> Mariam. >> >> >> On 31 Mar 2014, at 16:36, Douglas N Greve wrote: >> >>> On 03/31/2014 10:05 AM, Mariam Sood wrote: >>>> Hi Doug, >>>> >>>> I have a few queries regarding FWHM used in multiple comparisons >>>> correction program mri_glmfit-sim >>>> >>>> My data at present is analysed in FSL & Freesurfer following the procedure >>>> in the link >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer. No >>>> volume based smoothing at single subject level (in FSL) is done at the >>>> moment, and a 4 mm surface level smoothing was applied during mris_preproc >>>> stage. >>>> >>>> 1. I have noticed that mri_glmfit computed a FWHM of 8.578114 using >>>> residuals. How exactly is this value computed? >>> It is based on the correlation coefficient of the residuals of adjacent >>> vertices. >>>> 2. I understand that the cached simulation used in mri_glmfit-sim is >>>> selected based on the above computed smoothness value. Is this fine, or >>>> should I override? If I also smooth the data at the single subject level >>>> on the volume (in FSL), can I still follow the above process? >>> Do you mean over-ride because you smoothed at 4 but get 8.5? No, you >>> would use the 8.5. If you smoothed in the volume, depending on how much, >>> it is probably ok to continue the process (though technically not correct) >>> doug >>>> Many thanks, >>>> Mariam. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ___ >>>> 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
[Freesurfer] nifti1Read(): unsupported slice timing pattern 5
Hello everyone, I was trying out FS-FAST tutorial with my set of images (converted to NIFTI from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error 'nifti1Read(): unsupported slice timing pattern 5 in … '. Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added to cater for acquisition schemes in some siemens scanners (ours is siemens). Why doesn't Freesurfer like this? I looked through the Freesurfer mailing list, but didn't quite find a solution yet. I am new to whole fMRI analysis, so apologies if I am missing something obvious. Many thanks, Mariam. ___ 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] mris_preproc
Hello All, I am trying to do a cross-subject surface based analysis of data analysed using FSL. I am following the instructions in the following tutorial link. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer Each of my subject data comprises of two runs. My question is related to how to use mris_preproc to combine them. Can I combine together each of the runs of multiple subjects as below? mris_preproc --target fsaverage --hemi lh \ --out $OUT_DIR/xrun/lh.varcope$c.mgh \ --iv $subj[1]/run1.feat/stats/varcope$c.nii.gz $subj[1]/run1.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[1]/run2.feat/stats/varcope$c.nii.gz $subj[1]/run2.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[2]/run1.feat/stats/varcope$c.nii.gz $subj[2]/run1.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[2]/run2.feat/stats/varcope$c.nii.gz $subj[2]/run2.feat/reg/freesurfer/anat2exf.register.dat I understand that I can combine the gfeat output of each subject using mris_preproc. I am preferring above method as I believe it is more accurate. Please correct me if I am wrong. Many thanks, Mariam. ___ 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.
