Re: [Freesurfer] PET tools in FS dev v6.0

Hi Doug, I uploaded the files you requested. I'm not sure if it matters, but one thing I forgot to mention was that in order to get the pet file in the right format and orientation, I ended up using (ecattominc pet.v pet.mnc) and (itk_convert --inv-y --inv-x pet.mnc pet.nii). I couldn't find a goo

Re: [Freesurfer] total grey matter volume

I'm a fan of using global mean thickness as a covariate for thickness analyses, and total surface area as a covariate for surface area analyses.  That way you directly covary for possible global effects using the same type of measure that you are analyzing. cheers, -MH --  Michael Harm

Re: [Freesurfer] Parcellation stats

what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness a

Re: [Freesurfer] warping surface label to volume space

that is certainly wrong. What does it look like on the surface? You can upload the subject if you want and we will take a look On Mon, 28 Sep 2015, Jacobs H (NP) wrote: Dear Doug, By looking at it in Freeview. Anatomically, I would expect that the entorhinal cortex would not be localized so

Re: [Freesurfer] 3_group_comparison

Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command. Best, Ruopeng > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au Follow @neuraust

Re: [Freesurfer] 3_group_comparison

Many thanks!!!, yes, freeview has opened, but I am still not seeing any results, just the "lh.inflated" It says: "Failed to load surface overlay" and than I got the following message: bash-3.2$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG

[Freesurfer] Longitudinal_analysis

Dear Freesurfer Experts, I am trying to run a longitudinal analysis. I have done the first three steps of the analysis. Now, I am trying to visualize my results. However, I am having trouble doing the last step of the analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova bas

Re: [Freesurfer] 3_group_comparison

I think it needs a -f before the surface On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > Many thanks, yes, it did work well. > > But, than I ran "freeview > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 >

Re: [Freesurfer] 3_group_comparison

Many thanks, yes, it did work well. But, than I ran "freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d" and got the following message: bash-3.2$ freeview $SUBJECTS_DIR/fsaverage/surf/lh

Re: [Freesurfer] Multi-band slice time correction

It is in there for version 6 but not in 5.3. You can try using the new versions: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fsl ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/slicedelay slicedelay is a new program, but make sure to make a backup of stc.fsl

Re: [Freesurfer] Sulc value of given Tal coordinates

You can also map the sulc or curv to fsaverage. The coordinates (in freeview or tksurfer) are in MNI305 coordinates which are pretty close to Tal. doug On 09/28/2015 05:26 PM, Rudolph Pienaar wrote: > Hi Karen -- > > A given FreeSurfer surface can be thought of as a triangular mesh. This > mesh

Re: [Freesurfer] PET tools in FS dev v6.0

Can you upload the FS subject, pet data, and .lta? https://gate.nmr.mgh.harvard.edu/filedrop2 On 09/28/2015 12:08 PM, Jonathan DuBois wrote: > Hi Doug, > > I was told you were away last week so I'm reposting this message. > Thanks for sending me the information on the PET scripts. I > ran gt

Re: [Freesurfer] warping surface label to volume space

Something is definitely going wrong. Can you load the label as well and verify that the label itself looks ok? On 09/28/2015 05:32 PM, Jacobs H (NP) wrote: > Yes, here it is! > Thanks! Heidi > > > > Yes, here it is! > Thanks! Heidi > > > image1.png > > > > ATT1.txt > > > >> Op 28 sep. 2015 om

Re: [Freesurfer] Sulc value of given Tal coordinates

Hi Karen -- A given FreeSurfer surface can be thought of as a triangular mesh. This mesh contains many "points" (i.e. the vertex points of the constituent triangles). Each of these mesh vertex points contains many internal values, i.e. the x, y, z position of the point, the normal to the surfa

Re: [Freesurfer] warping surface label to volume space

Can you send a picture? On 09/28/2015 05:08 PM, Jacobs H (NP) wrote: > Dear Doug, > > By looking at it in Freeview. Anatomically, I would expect that the > entorhinal cortex would not be localized so laterally? And some voxels are > not in the temporal lobe. > > Best > Heidi > >

[Freesurfer] Multi-band slice time correction

Does/can Freesurfer support multi-band slice timing correction? Currently, I am applying slice timing correction with SPM however this seems to remove TR information from the resulting *.nii files which later breaks the FSFast pipeline. Many Thanks, Shaun -- Shaun Patel, Ph.D. Research Fellow

Re: [Freesurfer] .mgh file not load into surfstats

Great! Many thanks!! 2015-09-28 16:56 GMT-04:00 Douglas N Greve : > That template is part of the distribution, in > $FREESURFER_HOME/subjects/fsaverage > > On 09/28/2015 03:07 PM, Myriam Oliver wrote: > > Hi Bruce! > > > > I convert from the individual space to the talairach space, but the > > ta

Re: [Freesurfer] Parcellation stats

Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted be

Re: [Freesurfer] Parcellation stats

I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some th

Re: [Freesurfer] warping surface label to volume space

how are you determining that it is not in the right place? When I run this it works. On 09/28/2015 04:54 PM, Jacobs H (NP) wrote: > Hi, > > Bringing this to the FS list: > I am trying to warp the entorhinal cortex label (ex vivo) to volume > space, so that I can see and use the full ROI. Using t

Re: [Freesurfer] Convert volume to surface

> On 28 Sep 2015, at 13:14, Bruce Fischl wrote: > > I see. You can use mri_tesselate and mri_cc for this, probably followed by > some slight smoothing with mris_smooth, but it's not something we do > routinely. Emily (ccd) has done some work on vessel segmentation > specifically and might be

Re: [Freesurfer] .mgh file not load into surfstats

That template is part of the distribution, in $FREESURFER_HOME/subjects/fsaverage On 09/28/2015 03:07 PM, Myriam Oliver wrote: > Hi Bruce! > > I convert from the individual space to the talairach space, but the > target (--trgsubject) was the first subject from my data, that was > pick randomly

[Freesurfer] warping surface label to volume space

Hi, Bringing this to the FS list: I am trying to warp the entorhinal cortex label (ex vivo) to volume space, so that I can see and use the full ROI. Using the command stated below doesn’t seem to work, as it is not in the right location of the subject’s brain. Any thoughts? I used this command

Re: [Freesurfer] qdec error

Can you send the FSGD file? On 09/28/2015 02:06 PM, Lim, Lena wrote: > Sorry, please see error below: > > > > Reading /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl > > Using /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl > > Loading data table > /home/spjwk

Re: [Freesurfer] .mgh file not load into surfstats

Hi Bruce! I convert from the individual space to the talairach space, but the target (--trgsubject) was the first subject from my data, that was pick randomly. mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval talairach.white --tval-xyz --trgsubject ' subjectid01 I think it wi

Re: [Freesurfer] Parcellation stats

Hi Ali using Thomas' parcellation won't change the vertex-wise thickness values, but of course if you want to average within his ROIs you can generate stats files with that information. Sorry, does that answer you question? cheers Bruce On Mon, 28 Sep 2015, Ali Radaideh wrote: Thanks a

Re: [Freesurfer] .mgh file not load into surfstats

Hi Myriam sorry, I don't understand. What do you ean by "compare it with the cortical surface of fsaverage"? What are you trying to compare? cheers Bruce On Mon, 28 Sep 2015, Myriam Oliver wrote: Hi again! When I transform from the individual space to the average, I was doing it the comm

Re: [Freesurfer] .mgh file not load into surfstats

Hi again! When I transform from the individual space to the average, I was doing it the command line. To ensure the results are ok, I want to compare it with the cortical surface of the Freesurfer's average subject (fsaverage) Where can I find that template? Thanks in advance for your help and ti

Re: [Freesurfer] qdec error

Sorry, please see error below: Reading /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl Using /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl Loading data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of columns: 5 fsid column:

[Freesurfer] Error Messages for Accessing Bin

Hello, When I run the command "sFSstart" on version 5.0.0, I am receiving the messages below. Would you please explain to me what the problem is? It seems like there is trouble accessing the bin. Thank you freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Setting up environment f

Re: [Freesurfer] Parcellation stats

Thanks alot Douglas, Yes it is there but after checking it many time I found it corrupted for some subjects due to copying them many times between machines. But May I ask you some thing related. I have just posted a question regarding getting the cortical thickness after running the surf2surf com

Re: [Freesurfer] Parcellation stats

does that file exist? On 09/28/2015 01:05 PM, Ali Radaideh wrote: > Dear FreeSurfer experts, > After finishing the recon-all, I am trying to extract the cortical > thickness for each subject and group them into one table but > unfortunately i keep getting the following error: > > ​ rh.aparc.DKTa

Re: [Freesurfer] qdec error

He Lena, can you repost with the error message as part of the email instead of as a word doc file. doug On 09/28/2015 12:45 PM, Lim, Lena wrote: > > Sorry, I am re-posting below again for help… > > Dear Experts, > > I tried to see if the average area/thickness differ between the 2 > groups (HC

[Freesurfer] Parcellation stats

Dear FreeSurfer experts, After finishing the recon-all, I am trying to extract the cortical thickness for each subject and group them into one table but unfortunately i keep getting the following error: ​rh.aparc.DKTatlas40.stats is not found or is too small to be a valid statsfile Use --skip flag

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

Hi Thomas, I have done the mri_surf2surf all all old data and everything went OK. Thanks for your help. Now I need to extract the NEW cortical thickness based on this new parcellation. I am saying NEW because I extracted the cortical thickness last year without running the mri_surf2surf. We think

[Freesurfer] qdec error

Sorry, I am re-posting below again for help... Dear Experts, I tried to see if the average area/thickness differ between the 2 groups (HC and A) with IQ, Age and Gender as covariates using Qdec, but encountered the error (pls see attached). I tried the same thing for comparison between A and P

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

Hi Thomas, I have done the mri_surf2surf all all old data and everything went OK. Thanks for your help. Now I need to extract the NEW cortical thickness based on this new parcellation. I am saying NEW because I extracted the cortical thickness last year without running the mri_surf2surf. We think

Re: [Freesurfer] total grey matter volume

Yes, I would use it for all of those things. On 9/28/15 12:25 PM, Lim, Lena wrote: Thanks Doug. Do I include the TGM as a covariate only for between group comparisons? Do I need to control for it as well if I want to look at the correlation between surface area and age, clinical measures etc

[Freesurfer] Sulc value of given Tal coordinates

Hi I am not a Freesurfer expert or Matlab connoisseur. I am trying to find out how to get the Sulc and Curv value for a given tal coordinate. I was told that you load it in Matlab using read_curv, but how exactly do I do this, what does they syntax look like? I can see in the help this: [cur

Re: [Freesurfer] total grey matter volume

Thanks Doug. Do I include the TGM as a covariate only for between group comparisons? Do I need to control for it as well if I want to look at the correlation between surface area and age, clinical measures etc. within each group? Thanks again, Lena From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] total grey matter volume

Not for thickness. For surface area it is a good idea to do some kind of normalization. Typically people use the estimated intracranial volume (ICV). You can also use total brain volume or total grey volume. You just need to be aware that each one of these tests something different. On 9/2

[Freesurfer] total grey matter volume

Dear Experts, Do we need to include total grey matter volume as a covariate in the freesurfer cortical thickness and surface area analyses? I have come across papers that do and don't; so I am not sure if I have to do that. Please kindly advice. Many thanks, Lena

Re: [Freesurfer] PET tools in FS dev v6.0

Hi Doug, I was told you were away last week so I'm reposting this message. Thanks for sending me the information on the PET scripts. I ran gtmseg, and bbregister successfully (I inspected both and they look accurate), but I am getting a segfault with mri_gtmpvc at the auto mask step. I copied the

Re: [Freesurfer] Aparcstats2table Insula Thickness is Zero

Can you send the command and terminal output? On 9/24/15 2:23 PM, Popal, Haroon (NIH/NIMH) [F] wrote: Hello, When I use aparcstats2table to pull thickness values of the Desikan atlas, I get a value of zero for two of my subject’s insula thickness in both hemispheres. For these two subjects, I

Re: [Freesurfer] Question about the volume conversion in freesurfer

This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compu

Re: [Freesurfer] Query about the fsgd file and glm model in freesurfer

The 1st is wrong. The 2nd one is correct. You can also look at this page for more info include setting up contrasts https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V On 9/24/15 3:54 AM, chenhf_uestc wrote: Dear freesurfer experts, I have some questions about the statistical model in frees

Re: [Freesurfer] mri_vol2vol binary mask

Add --interp nearest to use nearest neighbor interpolation instead of trilinear On 9/24/15 1:48 AM, Jinsong Tang wrote: Hello, I am try to convert some binary mask (0,1) to native space. I use this command line: mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask _ra

Re: [Freesurfer] WMPARC fsaverage

Thank you Doug. On Mon, Sep 28, 2015 at 11:32 AM, Douglas Greve wrote: > > I made one and put it here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz > > Note that this should not be used for anything other than visualization, > ie, it has little or no scientific val

Re: [Freesurfer] PVE correction tool within the V 6 beta

I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions.

[Freesurfer] PVE correction tool within the V 6 beta

Dear Expert, Are there any explanation (steps to follow) about the use of FreeSurfer (version 6 beta) to correct for the partial volume effect (PET dynamic data)? Many thanks in advance, Best, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, Univers

Re: [Freesurfer] 3_group_comparison

Did you include the back slashes in your command? If so, remove them and retry. On 9/25/15 7:11 PM, Dusan Hirjak wrote: Dear Freesurfer experts, I am trying to compare 3 groups (aut, sch, ges) according to thickness, area and LGI at once (omnibus test). I did run the following command: mri

Re: [Freesurfer] WMPARC fsaverage

I made one and put it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz Note that this should not be used for anything other than visualization, ie, it has little or no scientific value On 9/24/15 6:25 PM, Mohammed Goryawala wrote: ​ Hello FreeSurfer Experts,

Re: [Freesurfer] dt_recon

On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote: Hi Doug and Bruce, After running the command : dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>> I need to generate the final statistics ( FA for every

Re: [Freesurfer] Convert volume to surface

Try using the mri_binarize below with the --surf option. You'll probably want to add a little smoothing with --surf-smooth 2 or so ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 9/27/15 4:58 AM, Martin Tisdall wrote: > Could you talk me through the best way to co

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Hi Bronwyn, you can probably drop the --cortex in the glmfit, as the --label should take care of that. I don't remember what is the best way of finding the subject with holes. I think you would - open the surface with intersect label with tksurfer, click into the hole to find a vertex that

Re: [Freesurfer] Convert volume to surface

I see. You can use mri_tesselate and mri_cc for this, probably followed by some slight smoothing with mris_smooth, but it's not something we do routinely. Emily (ccd) has done some work on vessel segmentation specifically and might be able to help with that. cheers Bruce On Mon, 28 Sep 2015,