[Freesurfer] Gray matter

Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calcula

[Freesurfer] Whole Brain definition

Hello Freesurfer experts, I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc

[Freesurfer] Xhemi stat questions

Dear Doug,I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.6

[Freesurfer] cortical recontruction error

Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz at this point:

[Freesurfer] offset in qdec GUI

Hi list, I have a question, probably trivial, on onset in qdec GUI. What's this? And what I can do using it? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor

[Freesurfer] correction on question: offset in qdec GUI

Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano --- Begin Message --- Hi list, I have a question, probably trivial, on onset in qdec GUI. What's this? And what I can do using it? Stefano ___

Re: [Freesurfer] Brodmann area thickness, surface area and volume

Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct thresh

Re: [Freesurfer] Whole Brain definition

Hi Ashkay, if you are doing voxel-wise TBM it probably doesn't matter. The definition of gray matter should be consistent between the two, just the labels of what bit of cortex they are will change. cheers Bruce On Fri, 22 Mar 2013, Akshay wrote: > Hello Freesurfer experts, > > I am currently

Re: [Freesurfer] correction on question: offset in qdec GUI

Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, std...@virgilio.it wrote:  Hi list, I have a question, probably trivial, on OFFSET in qdec GU

[Freesurfer] R: Re: correction on question: offset in qdec GUI

Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 22-mar-2013 13.48 A: Cc: Ogg: Re: [Freesur

[Freesurfer] Error with .license after upgrading to 5.2

Hi list, after upgrading to 5.2 (from 5.1), I am consistently getting a license error (see below). The strange thing is that my .license is the same file I was using on 5.1 and worked fine. I have also tried multiple modifications of file permission/owners (its a local install so I can be root

[Freesurfer] FreeSurfer 5.2 Segmentation & Talairach Registration Issues

Dear All, We have been running the recon-all pipeline in 5.2 and have been encountering some difficulties with segmentations. We have isolated these issues to problems with Talairach registrations, and have been re-running recon-all with the Talairach registrations manually corrected in tkregis

Re: [Freesurfer] FreeSurfer 5.2 Segmentation & Talairach Registration Issues

Hi Dan that sounds worrisome. I don't think we've seen this problem in our test cases. Can you upload an example so we can take a look? thanks Bruce On Fri, 22 Mar 2013, Daniel Carey wrote: > Dear All, > > We have been running the recon-all pipeline in 5.2 and have been encountering > some di

Re: [Freesurfer] Brodmann area thickness, surface area and volume

Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl : > Hi Andreia > > the issue is that the BA labels contain every point that has any non-zero > probability (no matter how small!) of bei

Re: [Freesurfer] Brodmann area thickness, surface area and volume

yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: > Hi Bruce, > > Thank you for the quick response! > > In the meanwhile, does that also apply to cortical thickness and volume? > > Thank you! > >

Re: [Freesurfer] help with contrasts

On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully wrote: > oops sorry! (I also miscalculated the # of regressors - there's actually > 12 (not 10 as previously noted). Here is the list of column labels: > Grp1male Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1 > Grp1maleVar2 Grp1femaleV

Re: [Freesurfer] help with contrasts

Thanks Donald for your help. One final question - putting the "does the amount of variance explained vary by group?" question aside, if I wanted to run a multiple regression style model within one group looking at the contribution of the two behavioral variables together, does it make sense to weig

Re: [Freesurfer] help with contrasts

You'd want an F test with 2 rows. One for the F-test of var 1 and one for the F-test of var2. A significant F-test won't tell you if your significantly better though than the F-test of var 1 only in the model. However, this sounds more like a model fitting question, which would be best addressed u

[Freesurfer] Talairach manual correction

Hello! After completing the talairach correction in tkregister2 (saving the changes with the SAVEREG button), I am running recon-all -all -s subj. But now I'm wondering if by doing it this way the changes will be incorporated or the process will start from the beggining leaving everything

Re: [Freesurfer] Error with .license after upgrading to 5.2

Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applicat

Re: [Freesurfer] help with contrasts

thanks for the clarification - I'll look into using other methods for model fitting. LT On Fri, Mar 22, 2013 at 8:46 AM, MCLAREN, Donald wrote: > You'd want an F test with 2 rows. One for the F-test of var 1 and one for > the F-test of var2. A significant F-test won't tell you if your > signifi

Re: [Freesurfer] Gray matter

Hi Jordi,I think you are looking for the information contained on the wiki:http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStatsTotalGray - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calcul

[Freesurfer] hippo subfield

I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02Actual FREESURFER

Re: [Freesurfer] Error with .license after upgrading to 5.2

Just use the license file from your previous version (or you can apply for a new license for free, but this is redundant). cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, respectively. Lingqiang > Hi - no luck un

[Freesurfer] R: R: Re: correction on question: offset in qdec GUI

If I'd like to show a contrast map between two group, which is the correct form? If I set offset=1 the red area will be more larger, with more results than offset=0, the the blue (negative) will be stable. If I apply the Montecarlo Sim the results will seem to be in accord to offset=0. Which is

Re: [Freesurfer] Gray matter

Hi Gabriel, I will try it! Thank you! 2013/3/22 Gabriel Gonzalez Escamilla > Hi Jordi, > > I think you are looking for the information contained on the wiki: > http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats > > *TotalGray* - total gray matter volume. This is simply the sum of SubCo

Re: [Freesurfer] Error with .license after upgrading to 5.2

Hi, that is exactly what I did (see my first message) - that's why I'm so puzzled! Nicola On 03/22/2013 05:05 PM, Lingqiang Kong wrote: > Just use the license file from your previous version (or you can apply for > a new license for free, but this is redundant). > > cp $OLD_FREESURFER_HOME/.lic

[Freesurfer] trac-all -prep exited with errors

Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTT

Re: [Freesurfer] trac-all -prep exited with errors

Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs. Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > Hi > I ran trac-all -prep -c dmrirc_single_subject > and got the following error: > > here's the end of the output from

Re: [Freesurfer] hippo subfield

Hi Stefano, Can you do "ldd kvlApplyTransform" and send us the result? Koen On 3/22/13, std...@virgilio.it processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n > kvlSegmentHippocampalSubfields.sh Diff02 left > /

[Freesurfer] R: Re: hippo subfield

I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: Cc: Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do "ldd kvlApplyTransform" and send us the result?

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts

Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data:

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts

Yes, the unique one. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stef

Re: [Freesurfer] trac-all -prep exited with errors

Hi Jon - The error says that it can't open a file *for writing*. Any chance it's a disk space issue or, if the file already exists, a permission issue? a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > HI Ansatasia > I have attached the trac-all.log > Jon > > - Original Message - > From: "

[Freesurfer] Two questions regarding mri_fill and mris_fix_topology

Dear FreeSurfers,   I am processing some T1-weighted images of the human brain with an isotropic resolution of .5 mm using version 5.1.   After mri_fill my hemispheres are separated nicely and the cerebellum is completely removed. However, looking at the filled.mgz, posterior and superior of th

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology

Hi Falk I don't think it's possible to fix just one defect, unless Florent included some option that I am not aware of. I also wouldn't worry too much about the filled.mgz. Make sure that the aseg.mgz and the ?h.white and ?h.pial are accurate cheers Bruce On Fri, 22 Mar 2013, "Falk Lüsebrin

Re: [Freesurfer] R: Re: hippo subfield

Hi Stefano, >From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: > I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should > do more simply? > > > Stefano > > > >

[Freesurfer] R: Re: R: Re: hippo subfield

>From command line I obtain: Stefano% ldd kvlApplyTransformldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem. Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: Cc: , Ogg: Re:

Re: [Freesurfer] R: Re: R: Re: hippo subfield

He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITK

[Freesurfer] R: Re: R: Re: R: Re: hippo subfield

otool: Command not found. Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: Cc: , , Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform:

[Freesurfer] R: Re: R: Re: R: Re: hippo subfield

[iMac-di-Stefano:freesurfer/subjects] Stefano% otool -L kvlApplyTransformotool: Command not found. Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: Cc: , , Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: o

[Freesurfer] problem with registration in preprocessing

Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen d

Re: [Freesurfer] trac-all -prep exited with errors

Can you run the flirt command that gives the error directly on the command line? On Fri, 22 Mar 2013, Jon Wieser wrote: > Hi Anastasia, > we have plenty of disk space, 386 GB > the file does not exist > > freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz > > the entire freesurfer directory

[Freesurfer] advice in registering a binary mask to Freesurfer space.

Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image.

Re: [Freesurfer] hippo subfield

Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was abl

Re: [Freesurfer] trac-all -prep exited with errors

It will, unless it doesn't find the anatomical segmentation of the subject ($SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz). On Fri, 22 Mar 2013, Jon Wieser wrote: > I ran the flirt command on command line and got the same error. > I noticed that the freesurfer/dlabel directory did not have an anatorig

[Freesurfer] QDEC issues

Hello everyone, I created a qdec.table.dat for my design (a simple group analysis, with gender as categorical factor and age as continuous factor), and created a gender.levels file containing the values that are found in qdec.table.dat, spellt in exactly the same way (all files attached). However,

Re: [Freesurfer] trac-all -prep exited with errors

Hi Jon - You will have to email the list with specifics about your recon-all problem, including recon-all.log. I can't guess what the problem is with no other information. I recommend starting a different email thread about it. a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > > there is not a ap

[Freesurfer] R: Re: hippo subfield

Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfieldsSubject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfe