Freesurfer

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30086 discussions

Problem of Volumes differ in dimension in Longitudinal pipeline
by wang kangcheng 07 Jul '14

07 Jul '14

Dear experts Today, I conduct the longitudinal analysis according to tutorials of freesurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) But, when I do recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all, it report the error: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mri_diff --notallow-pix /Users/wangkangcheng/Desktop/long_fs_test/long/s12002_MRI2/mri/rawavg.mgz /Users/wangkangcheng/Desktop/long_fs_test/long/s12002_MRI1/mri/rawavg.mgz \n Volumes differ in dimension v1dim 176 256 256 1 v2dim 176 184 200 1 \n******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- When I check the raw data and find that the structural data of s12002_MRI1 was the file which was converted by the command of dcm2nii and begin with "co". However, data of s12002_MRI2 was the file which begin with "o". But, when I used the file which begin with "co", they did not have same dimension. How could I solve the problem? (PS: have processed hundreds of data for subject of MRI1) Thank you Wang Kangcheng

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Using the Longitudinal Pipeline
by Alfred Ochs 07 Jul '14

07 Jul '14

Colleagues, We are preparing to perform longitudinal pilot studies a group of subjects and controls under far less than ideal conditions. The initial MRI scans were done clinically on a 1.5T Siemens scanner using the ADNI Siemens scanning protocol. The follow-up scans need to be done on a 3.0T Phillips (research, i.e., gratis) scanner using the ADNI Phillips protocol. Am I correct in assuming that the FreeSurfer longitudinal pipeline will somewhat iron out the inherent segmentation & parcellation differences between MRIs taken on these two machines? Thank you, Alfred Ochs

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mris__label__calc intersect error in longitudinal qcache
by Michael Kranz 07 Jul '14

07 Jul '14

Hi, I'm having trouble figuring out following problem: For one subject (out of 200), I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /SUBJECTS_DIR/sub2.long.subt/label/rh.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? *subt is base and sub2 is second time point .* Do you guys have any experience with this error and problems that it may have been caused by? I've tried re-running the longitudinal stream from scratch and the error still persists. I've visually checked the images and all segmentations were accurate. Thanks, Mike Kranz

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Categorical covariates with more than two levels on qdec
by Isotalus, Hanna 07 Jul '14

07 Jul '14

Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for the imaging site but qdec only allows me to covary for categorical variables if they have two levels (and I have eight). I am also using age (continuous) and gender (categorical, two levels) as covariates. Is there a way of using the imaging site as a covariate using qdec? Do you have any suggestions on how I should proceed? Is treating imaging site as a continuous variable acceptable? Best wishes, Hanna?

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Extracting polar angle and eccentricity from vertices
by Jackie Lam 07 Jul '14

07 Jul '14

Hello all, I’ve just finished retinotopy analysis following http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis…. Now I’m wondering, is it possible to get quantitative values of polar angle and eccentricity for each vertex from, say, an ROI I’ve drawn out? If so, how would I go about doing that? Which files would I use? Thank you in advance, Jack

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Get mean thickness after qdec monte-carlo simulation.
by June k. 07 Jul '14

07 Jul '14

Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas. Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation? -Sincerely, June.

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Overlay onto surf file
by Paul Quigley 07 Jul '14

07 Jul '14

Hello, Could anyone give me some insight into how freeview projects an overlay onto a surface? For example, I have an overlay generated though mri_vol2surf for subject pq, call it stats.nii. Opening the nifti in MATLAB, I see that the image it stores is a single, flat vector (had about 130,000 entries). I can overlay stats.nii onto a variety of surf files (e.g. sphere.lh, inflated.lh). So it seems clear that each surf file has its own method for translating the indices in the vector to points on the surface... Is there any way to extract this information from the surf file? Basically, my goal is to figure out how I can translate coordinates on sphere.?h (theta, phi or x,y,z doesn't matter) to subscripts on my T1. Any help would be greatly appreciated! Thank you, Paul

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Anterior Temporal Lobe / Pial Reconstruction Troubles
by Las Blawimo 07 Jul '14

07 Jul '14

Dear FreeSurfer Experts, We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T scanner. We're observing, in many subjects, a problem mentioned in previous posts to the list where the pial surface does not follow the cortex properly in the anterior temporal lobe region (and also in some frontal regions). The white matter surface generally looks very good. This is with the default options from recon-all in v5.3. We've also tried running the following options, based on previous posts (expert options) and the release notes for version 5.2: -norm2-b 20 -norm2-n 5 and -norm2-b 20 -norm2-n 5 -3T In general, there is a modest improvement in the medial temporal lobe pial surface in most subjects. A substantial/desired improvement is observed in only a few subjects. In general, there was no detrimental effect to either the white matter or pial surface when using these flags. Based on older posts to the list, we've also tried using the following flags: -mprage and -washu_mprage The improvement to the pial surface is much more substantial in almost all subjects, to some extent with the -mprage flag, mostly with the -washu_mprage flag. However, this dramatic improvement in pial surface accuracy was accompanied by many major issues with the white surface in widespread areas across the brain. Also, some subjects fail to reconstruct fully due to large defects in the surfaces with this option in place (also something I've read about happening to people using the -washu otpion on the list). A few questions: Would you suggest we also try the options "-norm1-b" and "-norm1-n" in addition to the norm2 options? If so, any suggested starting values to try? Alternatively, would it be sensible to try to use the white surface from the default pipeline and combine it with (or perhaps initialize) the pial surface from the -washu_mprage flag? Do you have other suggestions for us to try? Thank you for your time and help! Sincerely, Las

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Freesurfer Help
by Paras Patel 07 Jul '14

07 Jul '14

Dear Sir/Madam, I am a masters student at Newcastle University using Freesurfer to extract data from MRI scans. When trying to use the command lines in terminal, I seem to be getting an error message which I was wondering if you could help me with. The command line I am using is : recon-all -autorecon-all - subjid sam01 The error message displayed is: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh ERROR: Flag - unrecognized. -autorecon-all -subjid try01 Linux xubuntu-VirtualBox 3.2.4-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC recon-all -s exited with ERRORs at Mon Jun 23 06:47:34 EDT 2014 I have tried the help guide which suggest to update the VM and I have tried to uninstall and re-install Freesurfer but I still get the same error message. I also get the same error message when trying with a different subjid . Please can you give me further guidance on how to fix this error so that I can continue working with Freesurfer. Thank You, Kind Regards, Paras Patel Newcastle University

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Re: [Freesurfer] Fw: Problem with uploading Cluster Simulation data
by Douglas Greve 06 Jul '14

06 Jul '14

You should be able to view the map results in freeview just as you would any other map. doug On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* freesurfer(a)nmr.mgh.harvard.edu > *Betreff:* Problem with uploading Cluster Simulation data > Dear freesurfer experts, > we are conducting cortical-thickness analysis using freesurfer-4.4.0 > and the final analysis with qdec. I have a question concerning the > Clusterwise Correction for Multiple Comparison. > Is it correct that I have to visualize the results of the Monte Carlo > Simulation in freeview? > Do I have to upload a special model in freeview before uploading the > Cluster Simulation data? > Yours sincerely, > Carina

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