[Freesurfer] Book with FreeSurfer chapter
Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is "Automated Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalhães Oliveira Jr. et al. * ___ 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] how can do ''mri_convert''quickly when there are too many subjects
I suspect that your subject directory/file names will match some
pattern. You can use combination of a loop and shell "ls" command to
cycle through all the subjects matching provided pattern. For example
if you have data in directories you would do something line this:
#!/bin/tcsh
cd /path/to/native/files
for x in `ls -dA1 name_pattern_*`;
do
mkdir -p $SUBJECTS_DIR/${x}/mri/orig
$FREESURFER_HOME/bin/mri_convert ${x}.nii.gz $SUBJECTS_DIR/${x}/mri/orig/001.mgz
done
If all files are in the same directory substitute '-dA1' for "-A1" and
it should work. Note this assumes that you have nifti files, for DICOM
you will need to modify it further.
Cheers,
Jacek
2011/7/15 汪贵宏 :
> Hi Bruce,
>
> In our research,if there are 100 subjects,how can I process these data
> easily.For example，when I want to compare their thickness's difference，at
> first，I should do
> " mri_convert bert.nii bert.nii.gz",but when there are too many subjects,is
> there a way to do all of these 100 subjects at the same time?
>
> Many thanks,
> Wang
>
>
>
> ___
> 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.
>
>
___
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[Freesurfer] ERROR: dimension inconsistency in source data
Hi, I am sorry to re-post this problem, but I cannot find the source of my problem: During sampling the feat data to fsaverage using for example: mris_preproc --target fsaverage --hemi lh --out 3runs/lh.cope1.mgh --iv run1.feat/stats/cope1.nii run1.feat/reg/freesurfer/anat2exf.register.dat --iv run2.feat/stats/#cope1.nii run2.feat/reg/freesurfer/anat2exf.register.dat --iv run3.feat/stats/cope1.nii run3.feat/reg/freesurfer/anat2exf.register.dat For one subject I get in the log file: ... mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 3runs/tmp.mris_preproc.13727/1250.1.mgh --sval 3runs/tmp.mris_preproc.13727/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 132315 Number of value vertices = 132299 ... Does it mean that the recon-all files are incompatible with the functional images? Can this stem from some manual editing of pial surface? Where should I search to spot the problem? Thank you a lot, Aga ___ 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] DOF and smoothing in mri_glmfit
Dear Doug, I wanted to follow up on our discussion: I have re-run the analysis with the smoothing during the 1st level analysis and indeed the activation pattern looks more as we expect from the 3D analysis in FSL, although the regions that are "active" are the same. Thank you for your advice! Best, Aga On 7/7/11 5:14 PM, "Agnieszka Burzynska" wrote: > Thank you! I think I will just try it out: now run it as it is but also run > the 1st level with smoothing, as I need to add some contrasts anyway. Then I > should also know the difference between volume and surface smoothing. > Cheers, > Aga > > On 7/7/11 5:07 PM, "Douglas N Greve" wrote: > >> The problem with doing the smoothing at the first level in FEAT is that >> it will be volume-based, not surface-based. I'm not sure what to tell >> you about using the varcopes. They will certainly be very noisy without >> smoothing, so probably smoothing is a good idea, even if it's volume-based. >> >> doug >> >> Agnieszka Burzynska wrote: >>> Dear Doug, >>> Thank you so much. I completely see you point, but I have re-run the 1st >>> level feat without smoothing just because it has been recommended not to >>> smooth in the volume and then transfer it onto the surface, but rather first >>> smooth on the surface >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). >>> >>> What I plan to do in the end is to include the cortical thickness as the >>> vertex-wise covariate in the functional group analysis. >>> >>> So the final analysis will be on the group level, where, as you say, the >>> varcopes should not matter that much. >>> >>> However, I was also thinking of analyzing varcopes in addition to copes >>> (group analysis) to relate the variance of BOLD signal to the thickness. >>> >>> Would you then recommend going back and taking the initial 1st level >>> analysis with regular smoothing? >>> >>> Thank you! >>> Aga >>> >>> On 7/7/11 4:43 PM, "Douglas N Greve" wrote: >>> >>> Hi Aga, your commands look right. For the DOF, it should be the sum of the DOFs from all the runs (probably won't make much of a difference). Smoothing is a bit of an issue when you want to look at individual results. Technically, you should smooth before you do the first level analysis (ie, before your compute the varcope), but this would require doing the FEAT analysis directly on surface data. Smoothing after computing the varcope means that the varcope will not be accurate (it will be too large). The penalty is that you will see less activation than you should. At the group level, this is not such a big deal because you're either not using the varcope or you are using it as a weight. doug Agnieszka Burzynska wrote: > Dear all, > I am combining 3 runs of a subject using fixed effects GLM and I wanted to > make sure I am doing the right thing. > > For each subject I use: > mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof > 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label > $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 > > , while lh.cope1.mgh contains the concatenated cope1 images of the same > subject in fsaverage space (the same for varcope1). > > 1) Is it the right way? > 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it > correct? > 3) The functional data has not been smoothed in the 1st level analysis in > FSL (as recommended), and also not smoothed during sampling the copes to a > common space. Therefore I want to smooth it here for the first time, but > only with 5mm. Does it sound right? > > Cheers, > Aga > > ___ > 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] help on MAC ".licence" file
Hi: To register the freesurfer, I use the command "gedit .licence" and paste my registration information to it in ubuntu. It does works. However, I got a trouble when using MAC laptop. I don't know how to create the .licence file. I have got the registration information for MAC. I will be very appreciated if you can give me some clues and answers. Thank u very much.___ 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] how can do ''mri_convert''quickly when there are too many subjects
Hi Wang, You can try foreach s (subj1 subj2 etc) mri_convert $s.nii $s.nii.gz end Hope it works, Tanja. 2011/7/15 汪贵宏 : > Hi Bruce, > > In our research,if there are 100 subjects,how can I process these data > easily.For example，when I want to compare their thickness's difference，at > first，I should do > " mri_convert bert.nii bert.nii.gz",but when there are too many subjects,is > there a way to do all of these 100 subjects at the same time? > > Many thanks, > Wang > > > > ___ > 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] how can do ''mri_convert''quickly when there are too many subjects
Hi Bruce, In our research,if there are 100 subjects,how can I process these data easily.For example，when I want to compare their thickness's difference，at first，I should do " mri_convert bert.nii bert.nii.gz",but when there are too many subjects,is there a way to do all of these 100 subjects at the same time? Many thanks, Wang ___ 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.
