Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

paired analysis question
by Govindarajan, Koushik Athreya 21 Nov '13

21 Nov '13

Hi all, I am trying to compute differences between 2 runs of my same set of subjects (repeatability) using the steps from the paired analysis wiki page. After I finish the mris_preproc and the mri_surf2surf steps, when I do the glmfit, should I be using the osgm option ? Since it is the same subject, I do not need the age variable as mentioned in the 2nd fsgd file. If I should still be using the 2nd fsgd file and not osgm, what would my contrast file look like? Thanks for the help Koushik

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RAS, MNI305, Talairach, MNI-Talairach?
by Anita van Loenhoud 21 Nov '13

21 Nov '13

Hi all, I find myself getting quite confused about different coordinates systems. Is the following correct (when viewing in TkSurfer): RAS=MNI Talairach=MNI305 (they are all the same?) Talairach= (non linear) conversion from MNI305 Thanks, Anita

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help with save_nifti
by Leila Reddy 21 Nov '13

21 Nov '13

Hi, I am trying to save a nifti file using save_nifti. I'm running into a strange problem that I describe below. I have a nifti file (subj_mask.nii) created by a colleague using Nibabel (http://nipy.sourceforge.net/nibabel/) This volume is in the MNI305 space. Step1: In a first step I wanted to convert this volume to the fsaverage surface format. To do that I used : mri_vol2surf --src subj_mask.nii --hemi rh --out_type mgh --float2int round --o blah9-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage. I load it in tksurfer and when I do view-> configure->overlay, I see a range of values (as expected) and am able to set the min and max thresholds as I want. Step 2: In a second step I loaded this nifti file into matlab using load_nifti and had to alter the volume a little bit as below: hdr=load_nifti('subj_mask.nii'); vol=hdr.vol; vol(find(vol<4))=0; hdr.vol=vol; save_nifti(hdr,'new_mask.nii'). I convert the volume to fsaverage surface space as before but when I view it in tksurfer I am not able to set a min and max threshold with configure->overlay. Instead, there is no distribution of values plotted in the configure overlay window and I get the following error message: % ERROR updating histo: impossible limits (min 0.55556 >= max 0.55556) for axis "x" I finally managed to solve this problem by loading the header information from a FS-FAST created nifti: hdr_fsfast = load_nifti('bold/analysis.mni/mask.nii.gz'); hdr_fsfast.vol=vol; save_nifti(hdr_fsfast,'new_mask.nii'). Now I am able to see the distribution of values in the configure overlay window and am able to set the thresholds. The headers for FS-FAST and Nibabel generated niftis are indeed slightly different but why do I not have the problem in step 1 when I use the Nibabel file, but only in step 2 after I use save_nifti with the Nibabel header ? I use the load_nifti and save_nifti commands very often (and haven't had problems before because I was only using FS-FAST generated files) so I would really appreciate it if someone could point out what is going on so that I understand what to do in future. Thanks, Leila

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converting cortical labels into volumetric ROIs
by Mojdeh Zamyadi 21 Nov '13

21 Nov '13

Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-f… except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. "lh.parietal.nii.gz") looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh

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[freesurfer]Cohen'd effect size map
by 陈骥 21 Nov '13

21 Nov '13

> > Dear freesurfer experts > > > In qdec I use the DODS degsin to obtain the thickness difference between my two groups with age ,gender as nuisance.Then I want to get the effect size map instead of report the significance level. In freesurfer wiki I found that we can obtain the effect size map via gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study.While I have two groups,one control group with 25 subjects and one patient group with 25 subjects too,I doubt that which number I should use ,the number of patient group subjects 25 or for the whole subjects across groups 50 to repalce the Npilot in the equation? And then I look for previous relevant topic in the freesurfer mail list, found that doug suggested that we can get the effect size just use gamma/rstd, I tried for that but found completely different result between I use the equation of gamma/sqrt(gammavar*Npilot), which equation should I use for I want to get the Cohen'd effect size map? Thank you in advance for your helps! Ji Chen

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Re: [Freesurfer] Error when using --mask flag in mri_glmfit
by Douglas N Greve 21 Nov '13

21 Nov '13

The label will be totally off because it was not created in the conformed anatomical space of fsaverage. Does the mask look ok? If you want to view the label, use something like tkmedit -f $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz -ov sig.mgh -seg $SUBJECTS_DIR/fsaverage/mri.2mm/aseg.mgz doug On 11/19/2013 08:41 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > I use the following command to open tkmedit and then I load the mask, > the ocn.mgh file or the original label (created by mri_binarize) as a > segmentation (through the tkmedit menu). In this case a label does > open, but it is totally off. > > tkmedit fsaverage orig.mgz -aux brain.mgz -bc-main-fsavg -overlay > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol/omnibus/glm.amygdala/osgm/sig.mgh > -fthresh 2.3 -fmax 4 -aparc+aseg > > Thanks! > Suzanne > > > > > > > > > On Thu, Nov 14, 2013 at 8:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > What is your tkmedit command used to view the segmentation? > doug > > > On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote: > > Hi Doug, > > Thanks for the code, this works. Nevertheless, I am a bit > unsure about whether the masks that are used as input into > this command are correct. I like to check all the stages of > the process and when I open the mask.mgh file within the > appropriate glm folder, the segmentation is totally off (the > putamen is somewhere in the OFC). Furthermore, even though the > file that holds the output cluster from the Monte Carlo > simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems correct, the > segmentation file that I use as input into the mri_segstats > command is also totally off (mc-z.pos.23.lh.sig.ocn.mgh) when > I load it in tkmedit. Am I loading it incorrectly as a > segmentation? Does this have anything to do with the fact that > you advised me to use the 2mm version > fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my > tkmedit command? > > Finally, I also run into a problem with the nucleus accumbens > specifically. For some reason I get an error when I run the > glmfit and mc simulation within this specific mask. First I > make the mask: > > mri_binarize --match 26 --i > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz > --o > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz > > Then I run glmfit: > > set labels = (accumb) > foreach label ($labels) > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz > mri_glmfit-sim --glmdir glm.${label} --sim mc-z 10000 2.3 > mc-z.pos.23.lh --sim-sign pos > end > > But I get an error saying: > > FWHM = -nan > ERROR: input FWHM is NaN (not a number). > Check the mask in the glm directory. > > Any ideas what I am doing wrong? > > Thanks again! > > Suzanne > > > On Tue, Nov 5, 2013 at 12:04 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Hi Suzanne, there is probably an easier way to do this. If you > create contrasts of each condition vs baseline then run > isxconcat-sess on each, you can then run something like > > mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i > condition1.nii.gz --avgwf condition1.table.dat --excludeid 0 > > where condition1.nii.gz is the output of isxconcat-sess for > condition 1. The output fo mri_segstats will be > condition1.table.dat which will have a row for each > subject and a > column for each of the clusters > > doug > > > > On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote: > > > Hello again, > > I am stuck again in my analysis and I am not sure that > my code > is right. I want to do the following. With a Monte Carlo > simulation I search for significant clusters within a > particular ROI in my all conditions vs baseline > contrast. Then > I want to translate this functional cluster to each > individuals native space (as a label) and extract percent > signal change for each condition separately from that > label. > This is no problem in my surface analysis, but I am > not sure > how to do this in the volume. I ran the Monte Carlo > simulation > within the mask, which provides a segmentation called > mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would > be the > label that would go into mri_vol2vol to translate the > cluster > to native space. I found on the website, however, that you > need to use tkregister first. So I used the following > code, > but I am doubtful about whether I am doing this right. > > tkregister2 --mov > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol > /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s > ff_01_030512 --regheader --reg > ff_01_030512/register.dat --surf > > The results of this command do not look good at > all....(see > attached image). The cluster in the -mov file does not > overlap > with the amygdala. For the next step, I assumed to use > mri_vol2vol to save the cluster as a native space label, > although I'd like to make sure the first step is correct > before continuing with this step. > > mri_vol2vol --mov > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol > > /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh > --reg > ff_01_030512/register.dat --fstarg --interp nearest --o > ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512 > > > What am I missing? Is the translation off because I did > something wrong, or does that point to a deeper issue? > > > Any help is much appreciated! > > > Suzanne > > > > On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Hi suzanne, you'll need to use the 2mm version > fsaverage/mri.2mm/aseg.mgz > doug > > On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote: > > Hello all, > > > > I want to run a Monte Carlo simulation within a > volume > ROI and I am > > running into a problem when I use the --mask > flag while > running > > glmfit. My question is very similar to the > question asked in > > "[Freesurfer] Volume-based Monte Carlo > Restricted to a > within mask > > area" but I could not find the response to this > question. > > > > Here is my code. > > > > First, I created a volume mask with mri_binarize: > > > > mri_binarize --match 18 --i > > > > home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz > > --o > > > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > > > I checked the mask and it looked good. Then I > use the > mask in > glmfit. > > > > mri_glmfit --y ces.nii.gz --osgm --glmdir > glm.amygdala_lh --mask > > > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > > > When I do this, I get the following error: > > > > ERROR: dimension mismatch 1 between y and mask > > > > I guess this means that the ces.nii.gz file and mask > file don't > match, > > but I have no idea how to solve this. Any thoughts? > > > > Thanks! > > Suzanne > > > > > > -- > > > > Suzanne Oosterwijk, Ph.D. > > > > Postdoctoral Researcher > > > > Department of Social Psychology > > > > University of Amsterdam > > > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>>>va.nl <http://va.nl> > <http://va.nl> > <http://va.nl> <http://va.nl> > > > > > https://sites.google.com/site/suzanneoosterwijk/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>>va.nl <http://va.nl> > <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re global lgi values
by Anna Jonsson 21 Nov '13

21 Nov '13

Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796 2.9763 1.3967 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna

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aparc.DKTatlas40
by krista kelly 21 Nov '13

21 Nov '13

I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the difference between this and the apart.annot is? Does it just have 40 labels versus the 36 found in the older version? Thanks!

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recon-all -s subjects -all unexpected termination
by Rujing Zha 21 Nov '13

21 Nov '13

Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 21 Nov '13

21 Nov '13

Hi David - This log only shows output from the -path step and not from the -prep step. The file that's missing should be created during the -prep step, so there's no way to figure out what went wrong without seeing the output from the pre-processing. Please cc the freesurfer list on your reply. Thank you, a.y On Sat, 16 Nov 2013, David Soto wrote: > Thanks, please see attachedI only noticed this > ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg33_m > ni_bbr_cpts_5_std.txt > cheers > DS > > > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi David - Can you please send us the trac-all.log file for this > subject? > Without seeing where it stopped and what error messages there > are it's > hard to guess what's going on. > > Thanks, > a.y > > On Fri, 15 Nov 2013, David Soto wrote: > > > Hi - > > trac-all completed in all my Ps except one > > and I noticed that the dlabel/diff output does not contain > all the files > > > > I assessed whether it could be do to poor registration, by > checking > > the aparc+aseg > > file and looks allright > > > > I also checked the registration of FA maps to standard space > by > > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > dtifit_FA.bbr.nii.gz > > and seems fine > > > > also > > > > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz > > > > which also seems fine > > > > any ideas pls? > > > > thanks! > > > > ds > > > > > > > > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > I suspect the current problem is caused by poor > registration. > > Have you checked the aparc+aseg and/or the registration > from > > diffusion to anatomical and from anatomical to MNI? > > > > On Fri, 16 Aug 2013, David Soto wrote: > > > > > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > 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. > > > > > -- > http://www1.imperial.ac.uk/medicine/people/d.soto/ > >

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2004

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