Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

correcting rippled image
by Deirdre O Shea 02 Oct '12

02 Oct '12

Hey everyone, I was wondering if anyone knew how to correct for a ripple like effect in the image. I have adjusted the talairach and it still looks the same. Any suggestions would be great. see image attached. Thanks, Deirdre

2 1

Appropriate Segmentation Sequence?
by Sullivan, Patrick M. 02 Oct '12

02 Oct '12

Hello, I have a set of archival data (so I was unfortunately not able to specify the acquisition sequences and include the recommended MPRAGE sequence). I am asking which sequence (if any) would be most conducive to volumetric/regional analysis using FreeSurfer. A Philips Achieva 3.0T was used for all acquisitions. All patients all have a the following sequences: FLAIR (TE 140ms, TR 10ms, Flip 90) T2W_FFE (TE 16ms, TR 1.5s Flip 18) Spin Echo (TE 16ms, TR 600ms Flip 90) DUAL_TSE CLEAR (TE 13ms, TR 3.4s, Flip 90) Would any of these be appropriate for segmentation and volumetric analysis? Thank you very much. -Patrick

2 1

processing scans on more than one computer
by pietro de rossi 02 Oct '12

02 Oct '12

Dear FreeSurfer experts, I'm processing scans on three different computers and I would like to know if it is possible to collect all the processed scans together in order to analyze data on just one computer. I realized that even moving the processed subjects folders to another folder within the same computer (even if I set the new folder as the SUBJECTS_DIR) I'm not able to run tksurfer and tkmedit for those subjects....am I doing anything wrong? is it just that once you've processed the scans the proc_folders cannot be moved? thanks, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

2 4

Average Thickness in QDEC
by Antonella Kis 02 Oct '12

02 Oct '12

Dear Experts, What is the best way to get the average thickness for each subject in QDEC, more exactly for the uncorrected clusters? I know when running QDEC theer is a stats_tables file saved so I wonder if the lh. aparc.thickness.stas.dat represents the mean cortical thickness. Should this values be the same with my thickness values under cache.th20.abs.y.ocn.dat obtained by running the mri_glmfit-sim with the option --cache where in order to catch all the clusters since I need the uncorrected one I used --cwpvalthresh .999? Thank you for you time and clarifications. Best regards, Antonella

1 0

Lesioned brain (surface) registration to fs average
by octavian lie 02 Oct '12

02 Oct '12

Dear all, I need to mark the cortical extent of a lesion (intersection of the lesion and pial surface, where "lesion" represent a epilepsy related resection). After the pial labeling of the resection, I need to register the labeled surface to the fsaverage. I completed recon-all routine on the postop T1, and went nicely, corrected pial surface in a few places. Question: what is the best way to mark the pial extent of a resection? Is there a way to accurately register the lesioned pia to the fsaverage, potentially by masking the resection ROI? Thank you for your insight, Octavian.

2 1

ADC map negative values
by Efrat Kliper 01 Oct '12

01 Oct '12

Dear FreeSurfers Users, When i am using the dt_recon function to create adc map i get quite a lot negative values, dose anyone encounter this problem? Thanks, Efrat

1 0

random effects analysis with performance values
by Maryam Vaziri Pashkam 01 Oct '12

01 Oct '12

Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam

3 5

Triangulated surfaces
by Efrat Kliper 01 Oct '12

01 Oct '12

Dear FreeSurfer Users, I have created a binary mask for the hippocampi and now i want to create the triangulated surfaces of the hippocampi? An one know how to do it? Thanks, Efrat

2 1

Error with mri_volcluster
by Antonella Kis 01 Oct '12

01 Oct '12

Dear Doug, I was running the mri_glmfit-sim \ --glmdir GroupAnalysis_abs.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign abs \ --cwpvalthresh .05 just to get an idea of how my FA Group Analysis data is looking and I got an error before to get the permcsd.sig.cluster.summary file from the mri_volcluster: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz I replaced the fsaverage/mri/aparc+aseg.mgz with the cvs_avg35/mri/aseg.mgz and to get the cluster summary I was running: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh but then I am getting the following error: NOT Adjusting threshold for 1-tailed test Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: GroupAnalysis_abs.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 961260 Found 961260 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. Can you please help me to solve this problem. I am not sure what to do. Thank you very much! Antonella PS. Just to remember you that I registered my FA data over the CVS space but I have for each subject from dt_recom the register.dat file so I suppose I need to keeo the fsaverage in the --reg COMMAND-LINE ARGUMENTS.

3 2

Re: [Freesurfer] mri_glmfit-sim with pre-cached fails
by Ed Gronenschild 01 Oct '12

01 Oct '12

Doug, For the PCA residuals we found 37% for the first component. The same analysis has been done for FreeSurfer v4.5.0, and we found a residual FWHM of 15.27 and 30% for the first PCA component. The time courses showed some outliers for both versions, very much dependent on the position on the surface, i.e., each time different subjects were outside the confidence limits. Summarizing: v4.5.0: residualFWHM = 15.27; 1st PCA 30% v5.0.0: residualFWHM = 34.00; 1st PCA 37% (number of subjects is 53). So, it is a puzzle why the residual FWHM is that large for v5.0.0. Ed On 1 Oct 2012, at 9:15, Ed Gronenschild wrote: > > On 28 Sep 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu > wrote: > >> Message: 27 >> Date: Fri, 28 Sep 2012 10:03:47 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <5065AE43.7060103(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hmmm, that's a lot, but I'm very surprised that the final FWHM is >> over >> 30. How many subjects do you have? There might be one that is >> messed up. >> You can check this by loading the y.mgh as a "time course" in >> tksurfer. >> It will give you a graph with each subject. Finally, you can run >> mri_glmfit with the --pca option to get a PCA of the residuals. This >> will create a folder called pca-eres. Look at the stats.dat and >> see how >> much variance is explained by the first component (first row, 4th >> column). >> doug >> >> On 09/28/2012 03:31 AM, Ed Gronenschild wrote: >>> Hi Doug, >>> >>> For mri_glmfit I used a cortical thickness smoothed with a FWHM >>> of 20, >>> resulting from using the -qcache option in recon-all. >>> >>> Ed >>> >>> On 27 Sep 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: >>> >>>> Message: 16 >>>> Date: Thu, 27 Sep 2012 11:29:06 -0400 >>>> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>> Message-ID: <506470C2.5060906(a)nmr.mgh.harvard.edu >>>> <mailto:506470C2.5060906@nmr.mgh.harvard.edu>> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> Hi Ed, when I created the cache, I only went up to 30mm FWHM >>>> thinking >>>> that no one would ever go above it, or maybe should never go >>>> above it. I >>>> can create tables at higher smoothing levels, but 34mm is a lot of >>>> smoothing. How much did you apply to the data? >>>> doug >>>> >>>> On 09/27/2012 05:48 AM, Ed Gronenschild wrote: >>>> >>>>> Hi, >>>>> >>>>> I want to apply a cluster correction with mri_glmfit-sim with >>>>> the --cache option: >>>>> mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs >>>>> It fails with the error message that it can't find the file: >>>>> FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/ >>>>> th1.3/mc- >>>>> z.csd >>>>> (FSDir is the directory where FreeSurfer is located, >>>>> version 5.0.0, Mac OSX10.5) >>>>> Looking at the content of the ....fsaverage/lh/cortex directory >>>>> than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 >>>>> are present. >>>>> In the log file from mri_glmfit I can read that the residualFWHM >>>>> is 34.005014. Since this FWHM is automatically derived by >>>>> mri_glmfit, does it mean that I can never use the --cache option >>>>> in this case? > >>>>> Cheers, >>>>> >>>>> Ed >>>>> >

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer