Re: [Freesurfer] Artefactual skull stripping for some subjects

Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance! Tudor On 5 July 2013 17:26, Tudor Popescu wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I noticed that there are artef

Re: [Freesurfer] Error after recon_all on pre-BETed image

Hi Richard did you "conform" (resample to 1mm isotropic, 256^3, 8 bits/voxel) your skull stripped image? That's probably what's causing you problems. You can do this with mri_convert cheers Bruce On Mon, 8 Jul 2013, Lin, Richard Lee-Tsong wrote: Hi Bruce, Thanks for the advice. The recon

Re: [Freesurfer] Artefactual skull stripping for some subjects

Hi Tudor the T1.mgz is intensity corrected and conformed (the orig.mgz is just conformed). Have you read the documentation on fixing skull strip problems on the wiki? cheers Bruce On Mon, 8 Jul 2013, Tudor Popescu wrote: > Dear FSers, > > Still haven't got to the bottom of this, any suggestio

Re: [Freesurfer] recon-all

Hi Bella it looks like it finished without error, in which case the thickness values will be stored in "curvature" format in the files $SUBJECTS_DIR/$subject/surf/[lr]h.thickness cheers Bruce On Sun, 7 Jul 2013, wrote: > Hi expert, > When I excuted the recon-all,I got the result that the

[Freesurfer] Tumor segmentation...

Hi all, I Have MRI scans (T1/T2/Flair) with (manually) segmented tumors and I would like 2 use Freesurfer to estimate the brain locations of those Tumors. (I.e. What area of the brain "affected" by these tumors) .. Of course thisis not for clinical use, but "research" -- Is this task possible w

Re: [Freesurfer] Tumor segmentation...

Hi Dov sure, run your T1 through recon-all, then use bbregister to register whatever image(s) were used to manually label the tumor to the anatomicals and go from there cheers Bruce On Mon, 8 Jul 2013, Dov Sadan wrote: Hi all, I Have MRI scans (T1/T2/Flair) with (manually) segmented tumors

[Freesurfer] Xhemi results

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of eac

[Freesurfer] Loading T1 maps onto inflated surfaces

Hi, I am new to FreeSurfer and I'm trying to figure out how to view T1 volumes on inflated surfaces in FreeSurfer. Any guidance would be appreciated! Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed

Re: [Freesurfer] Painting voxels vs. adding control points

Dear Bruce and freesurfers, Someone has suggested to me that my problem is a result of the poor resolution of the original MPRAGE data. If I know that my volume index of a problematic point is (152,91,124), how can I map it onto my original MPRAGE data and check? Thank you very much! Sincerely,

Re: [Freesurfer] Exporting freesurfer images

Dear Bruce, Thank you very much! Sincerely, Ye On Fri, Jul 5, 2013 at 8:59 AM, Bruce Fischl wrote: > Hi Ye > > you can use tcl to script it, or use freeview which I think can save > slice-flythroughs as a movie. > > cheers > Bruce > > On Fri, 5 Jul 2013, ye tian wrote: > > Dear Freesurfers, >

Re: [Freesurfer] Questions regarding QDEC

On 07/07/2013 01:36 PM, jh kim wrote: > Dear FreeSurfer experts... > > Please be patient with a newbie's questions. > For the first time, I'm trying to analyze between-group differences in > cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. > I've read through the online manu

Re: [Freesurfer] color scale for longitudinal analysis using freeview

Dear experts, Could someone point me to the color key for the output of the longitudinal analysis as viewed in freebies (as generated by the freesurfer longitudinal analysis tutorial)? Thank you, Sal Salil Soman, MD, MS ___ Freesurfer mailing list Fre

Re: [Freesurfer] Exporting data from "Find Clusters and Goto Max"

On 07/06/2013 10:19 PM, Sean Hatton wrote: > Hi all, > > Within QDEC, when I click on the "Find Clusters and Goto Max" button I > can see the individual thickness values per datapoint. > > 1. I am co-vaying for age: would these values be raw thickness values > or estimated margin means? Raw thic

Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 41

Hi Maria, sorry for the delay. Can you tar up your three QDEC output directories and drop them to us on our filedrop system? https://gate.nmr.mgh.harvard.edu/filedrop2 thanks doug On 07/08/2013 09:48 AM, Maria Kharitonova wrote: > Hi, sorry I must have missed the response to this a few weeks

Re: [Freesurfer] Artefactual skull stripping for some subjects

Thanks Bruce. I have looked at that part of the wiki but I was wondering whether the screenshots at all suggest that all artefacts are likely to be the result of the same problem, and that e.g. re-running recon for all subjects with a watershed>25 and with the -no-wsgcaatlas flag might be the thing

Re: [Freesurfer] importing from nifti

would it be possible to use volumes generated from recon-all -s into the second and third steps of the longitudinal processing workflow? On Tue, Jul 2, 2013 at 2:24 PM, Martin Reuter wrote: > In the meantime you can check how the mri/orig/001.mgz and the > mri/orig.mgz and mri/orig_nu.mgz look

Re: [Freesurfer] Error for mri_glmfit contrast

Hi Catherine, this usually means that something funny is going on with the contrast matrix. Eg, you made the contrast under windows? If so, then make it again under linux. If not , then send the contrast file doug On 06/24/2013 09:52 AM, Catherine Bois wrote: > Dear Freesurfer experts, I am cur

Re: [Freesurfer] mri_glimfit paired analysis

Hi Gayane, I don't know whether I answered this or not, but you will need to add "--surface fsaverage lh" to your command line doug On 06/24/2013 12:18 PM, Gayane Aghakhanyan wrote: > Dear FreeSurfers > > I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. > Currently running paired analysis as descr

[Freesurfer] Registration of FLAIR to MPRAGE

Dear all, I want to obtain mean intensity value for each segment (GM, WM, subcortical) from FLAIR images. Now I have processed the MPRAGE image (same subject) using "recon-all". The next step I figured is to register the FLAIR image to the MPRAGE and transfer the segmentation of MPRAGE to FLAIR, a

Re: [Freesurfer] Is there any way of finding out RESEL number in the GLM output?

It should be possible to compute from the FWHM, but I don't know how to do it off the top of my head. I'll keep it in mind the next time I update mri_glmfit. doug On 06/24/2013 03:05 PM, Glen Lee wrote: > Hello Freesurfer users, > I'd hope to know the RESEL number in my group GLM analysis da

Re: [Freesurfer] Registration of FLAIR to MPRAGE

Use bbregister. Run it with --help for help and examples doug On 07/08/2013 12:49 PM, Xinyang Liu wrote: > Dear all, > > I want to obtain mean intensity value for each segment (GM, WM, > subcortical) from FLAIR images. Now I have processed the MPRAGE image > (same subject) using "recon-all". Th

[Freesurfer] Cutting into a surface of grey matter

Dear Freesurfers, When an image cuts through a surface of grey matter (e.g. attached Freesurfer.png), will freesurfer overestimate cortical thickness? If so, how do you go about editing the image? Thank you very much! Sincerely, Ye <>___ Freesurfer mai

[Freesurfer] likelihood of identical subcortical volumes

hi, trying to figure out the likelihood of identical subcortical volumes across individuals. i'm noticing this in some data processed with FreeSurfer 5.1.0. just to give some probabilities - these are out of about 963 participants. and there are several such small clusters of identical numbers -

Re: [Freesurfer] Artefactual skull stripping for some subjects

001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: > Thanks Bruce. I have looked at that part of the wiki but I was > wondering whether the screens

Re: [Freesurfer] Cutting into a surface of grey matter

why do you say it's cutting through gray matter there? From the image it looks pretty accurate to me On Mon, 8 Jul 2013, ye tian wrote: > Dear Freesurfers, > When an image cuts through a surface of grey matter (e.g. attached > Freesurfer.png), will freesurfer overestimate cortical > thickness? I

[Freesurfer] Longitudinal processing

As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s for the second and third steps of the workflow. jon ___ Freesurfer mailing list Freesurfer@nm

Re: [Freesurfer] Longitudinal processing

In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: > As I'm having trouble importing nifti files in

Re: [Freesurfer] Longitudinal processing

Allison I'm running the followingrecon-all -all -s -i path/to/nifti attatched is the error recon log I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and

Re: [Freesurfer] Longitudinal processing

I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison On Mon, 8 Jul 2013, Jonathan Holt wrote: Allison I'm running the following recon-all -all -s -i path/to

Re: [Freesurfer] importing from nifti

Yes that is done that way. I thought you wanted to rerun the cross sectional data from scratch. But you can use your existing setup and run base and long on top of it. But avoid mixing freesurfer versions if posdible. Best martin  Sent via the Samsung Galaxy S™ III, an AT&T 4G LTE smartphone

Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 41

Hi Maria, I've tracked down the source of the difference. In 5.0, mri_glmfit simply takes whatever matrix you give it regardless of how well or badly conditioned it is. In your case, your matrix is badly conditioned because the scaling between the columns is very different. Eg, the 5th column

[Freesurfer] application of mri_cvs_register question

Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I'm not clear on how to do so to DTI data processed in Tracula. The command in the "Multimodal integration and inter-subject registration" tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg

Re: [Freesurfer] likelihood of identical subcortical volumes

a quick update. the following fiddle will show the number of subjects that have an identical the same Right Amygdala volume. It simply plots a histogram of the counts per volume (scroll to the bottom of the result window). http://fiddle.jshell.net/satra/MXKY6/6/ cheers, satra On Mon, Jul 8, 20

Re: [Freesurfer] likelihood of identical subcortical volumes

Hi Satra this seems vanishingly unlikely to me, particularly with partial volume correction. Have you visualize some of the subjects that have the same structure volume? Bruce On Mon, 8 Jul 2013, Satrajit Ghosh wrote: > a quick update. the following fiddle will show the number of subjects that

Re: [Freesurfer] likelihood of identical subcortical volumes

hi bruce, i visualized these two subjects using freeview and nothing looked out of the ordinary. $ cat /mindhive/xnat/surfaces/adhd200/3684229/stats/aseg.stats | grep -i amy 13 18 1764 1764.0 Left-Amygdala 64.7514 7.583136.90.54. 28 54

Re: [Freesurfer] likelihood of identical subcortical volumes

I believe it does, although the integral values are a bit suspicious. Maybe Doug or Nick knows? On Mon, 8 Jul 2013, Satrajit Ghosh wrote: hi bruce, i visualized these two subjects using freeview and nothing looked out of the ordinary. $ cat /mindhive/xnat/surfaces/adhd200/3684229/stats/aseg.st

[Freesurfer] average/RB_all_2008-03-26.gca not found error

Hi, *Am running this command:* $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all *And am get this out put / error:* Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVID

[Freesurfer] qdec control variable limitation

Dear all, I am using qdec to do a shape analysis with 16 control variables. I was wondering if there is a limit on how many covariates can be used in qdec? Because it seems that I cannot select all my covariates in "nuisance factors". Thanks and regards, Jiyang ___