[Freesurfer] Hippocampus subfield

Dear experts in Freesurfer, I am doing analysis on hippocampus subfield and I'm wondering if I could obtain cortical thickness data from each segmentation? Thanks so much! Best, Ariel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Reporting age differences between groups

Hi, I need a general advice from the experts out there. I am comparing cortical measures (thickness and volume) between controls and patients using FreeSurfer. I used 'age' and 'gender' as covariates (in fsgd file) while calculating group differences. I was wondering even if I removed the

Re: [Freesurfer] Pial surface editing

are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards. On Wed, 9 Aug 2017, Michelle VanTieghem wrote: -bash-4.1$ mri_info orig.mgz Volume information for orig.mgz           type: MGH     dimensions: 256 x 256 x 256    voxel sizes: 1.,

Re: [Freesurfer] convert mgh to nii problems - cannot get output file to reshape properly

Can you send me the file? On 08/09/2017 04:17 AM, Suzanne Witt wrote: > Hi. > > I am having a problem similar to that previously described on the freesurfer > message boards from May 2011 (Subject: mgh conversion). Unfortunately, that > thread ends with Doug asking the person to send him the

Re: [Freesurfer] ROI labeling?

You can map the ROIs into fsaverage space as binary masks, then average them together, then binarize the average (you'd have to pick the threshold). You cannot give mri-glmfit mutliple labels, but you can merge the labels together (mri_merge_labels) On 08/04/2017 03:13 PM, Sadie Marvel

Re: [Freesurfer] Pial surface editing

-bash-4.1$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Hmm, if you run: ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz what does it show? > On Aug 9, 2017, at 4:47 PM, Z Hessam wrote: > > of course: > > hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v > bert/mri/T1.mgz

Re: [Freesurfer] Optseq2 timing outputs

sorry, I thought I answered this. those slight offsets are not important, you can round to nearest TR On 08/08/2017 10:57 PM, Ruthie Shaffer wrote: > Hi all, > > I sent a message previously and just wanted to check in one more time > about this question (apologies for the repeat message!). > >

Re: [Freesurfer] Talairach error

It is failing the tal registration check. Does the registration look ok? If so, then run with -no-talcheck. On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote: > Hello FreeSurfer experts, > > I have been running into a consistent problem of Talairach alignment > error in my recon-all for some of

Re: [Freesurfer] Freesurfer PIB PET image processing

We do not have any thing to specifically analyze PiB. You can look at the PETsurfer page for more general instructions On 08/09/2017 02:15 AM, M Janani wrote: > > Hi Team, > > I apologize, I am new to Freesurfer. > > Currently we are processing PIB PET images. > > When we

Re: [Freesurfer] VBM

we do not support vbm processing On 08/08/2017 06:21 PM, Shane S wrote: > Hello Experts, > > Can we do VBM in MNI template using the outputs from recon all? Which > file should I be using? And how do I smooth the volumes? > > Thank you for the tips! > > -- > Shane S > > >

Re: [Freesurfer] Sphere above a certain vetex

A sphere or a circle? If circel, you can create a delta functon (a map on the surface where everything is 0 except your vertex which is 1.0) with mri_volsynth, specify the delta column to be your vertex number. Then smooth with mris_fwhm, then threshold with mri_binarize at some very low value

Re: [Freesurfer] Generating Surfaces from Labels

On 08/08/2017 03:42 PM, Zach Humphrey wrote: > Hello All, > > I have been attempting to convert Label files generated using > mri_annotation2label into surface files for use in external programs. > In order to do this I first need to convert the label files into > freesurfer binary. I have

Re: [Freesurfer] ASL with rcbf-prep

Hi Lauri, this program is not being supported anymore, sorry:) doug On 08/08/2017 02:20 PM, Tuominen, Lauri Johannes wrote: > Dear freesurfers, > > I have data collected here at the martinos using the Siemens ep2d_PASL > sequence. I run the command "rcbf-prep —s subject —rcbf asl.nii —o

Re: [Freesurfer] question about effects of changing server and freesurfer versions IF the entire study is consistent

There will certainly be differences between 5.3 and 6.0. Changing the OS will probably have minor effects. On 08/08/2017 12:24 PM, STACEY M SCHAEFER wrote: > > Hello Freesurfer experts, > > > We have processed, hand-edited, and QA'ed over 130 subjects' scans > with version 5.3.0 on a linux

Re: [Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis

can you send the design matrix Xg.mtx and the full terminal output? On 08/08/2017 09:13 AM, Sullivan, Danielle Renee wrote: > > Hi FreeSurfer Experts, > > > I am trying to run a dods cortical thickness analysis examining the > interaction of group on a continuous variable while controlling for

Re: [Freesurfer] Extracting pial surface from manually pareclated atlas

do you mean the pia tissue (which we can't do) or the pial surface, which is a surface and not in aparc+aseg On 08/07/2017 06:59 PM, Almarshad F. wrote: > Hi freesurfer team > > I'm just wondering if there is any way to extract left and right pial from > manually parecllated file apar+aseg

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

make sure you pass the full path to the fsgd, otherwise it looks in the current folder. Also make sure it is readable by you On 08/09/2017 05:12 PM, Nick Corriveau-Lecavalier wrote: > > Hi Freesurfer team, > > > I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) > with 0

[Freesurfer] GLM error - cannot read fsgd file for reading

Hi Freesurfer team, I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) with 0 covariables at the moment, but I would like to add two eventually. I've been following the tutorial on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write the

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

of course: hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue

Re: [Freesurfer] Pial surface editing

can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails? thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi,  I originally used  mri_convert orig.mgz

Re: [Freesurfer] Pial surface editing

Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Can you copy and paste the exact command line you ran and the error message? Ruopeng On 08/09/2017 02:21 PM, Z Hessam wrote: I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject? On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl

Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

they probably aren't from the right dicom series then. On Wed, 9 Aug 2017, Yagmur Ozdemir 19 wrote: > I tried that and realized the images are very blurry so it probably will not > run in any case. > > Thank you! > Idil > > From:

Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

I tried that and realized the images are very blurry so it probably will not run in any case. Thank you! Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu]

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

can you try it without all the \ characters? You shouldn't need them if it's all on one line On Wed, 9 Aug 2017, Z Hessam wrote: $>freeview -v \    bert/mri/T1.mgz \    bert/mri/wm.mgz \    bert/mri/brainmask.mgz \    bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

$>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \ bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \

[Freesurfer] "failed to load mri" in terminal, not in GUI

Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \

Re: [Freesurfer] Gcuts erasing voxels within the ventricles

Hi Elijah gcuts is a contributed tool (from Mike Chee's lab) and not one that we wrote, so I don't think we can help. sorry Bruce On Wed, 9 Aug 2017, Elijah Mak wrote: Hi Freesurfer Team, I am using gcut to improve the skull stripping on some subjects. I noticed that it is also removing

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[Freesurfer] PhD Scholarship at Aston Brain Centre (UK)

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Re: [Freesurfer] Total White matter and CSF value Calculation

Thanks Douglas From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 02 August 2017 21:15 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Total White matter and CSF value Calculation The first formula is

[Freesurfer] Gcuts erasing voxels within the ventricles

Hi Freesurfer Team, I am using gcut to improve the skull stripping on some subjects. I noticed that it is also removing some of the voxels in the ventricles of the brainmask.mgz (picture attached). Is this normal behaviour?  Thanks for your time. Best Wishes, Elijah 

[Freesurfer] convert mgh to nii problems - cannot get output file to reshape properly

Hi. I am having a problem similar to that previously described on the freesurfer message boards from May 2011 (Subject: mgh conversion). Unfortunately, that thread ends with Doug asking the person to send him the files in question, so there does not appear to be any sort of publicly published

[Freesurfer] Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume

Hello all FYI I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my healthy young sample It is probably due to the cerebellum computation changes (presented in released notes for 6.0) Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar (all was

[Freesurfer] Freesurfer PIB PET image processing

Hi Team, I apologize, I am new to Freesurfer . Currently we are processing PIB PET images. When we compare the SPM data along with FREESURFER outputs. We were able to see a large variation in the values. Could you please guide us in processing