Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

Different volumes in ?h.aparc.stats and wmparc.stats
by Wayne Su 23 Apr '09

23 Apr '09

I looked into the ctx volumes reported in ?h.aparc.stats (such as frontalpole) and the same one in wmparc.stats (labelled as ctx-?h-frontalpole). The volumes are slightly different. I am wondering why this happened and which one is better. Thanks. Wayne

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mouse/rodent neuro-imaging data analysis
by Siddharth Srivastava 23 Apr '09

23 Apr '09

Hi everyone, I would like to get the opinion of the users on this, regarding the feasibility of using freesurfer for analyzing mouse imaging data, provided that we have at our disposal, a supporting atlas. I know that Caret provided a fine scale parcellation for this species. Are there users on this list who have developed a working pipeline that uses freesurfer as one of the components to process such a data? It would be a great help if i can hear from some of you on the most optimal (open source/freeware) way of going about it. I am currently inclined towards using freesurfer+caret+slicer as enabling components for the analysis. Amy thoughts would be highly appreciated. best regards, sid.

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Re: [Freesurfer] t4_read error (fwd)
by Zhen Zonglei 22 Apr '09

22 Apr '09

Dear Avi: Thanks for your kind and the script.I will use it to check tal QC of all my data . Zognlei 2009/4/21 Avi Snyder <avi(a)npg.wustl.edu> > Zonglei, > > 1. Re: how to detemine Talairach transform success from the logfile: > Attached is a simple csh script (tal_QC_AZS) and a required awk script. > tal_QC_AZS reads the log file and writes out two numbers. > The first number (eta) is the spatial correlation between the (blurred) > input > image and the atlas representative target image. eta values less than 0.96 > are highly > suspect. The second number ("atlas_transform_error") is computed on the > basis of > registration objective function curvature in parameter space. The 12 > present numbers > are compared to values derived from a training set. atlas_transform_error > values > less than ~15 are good. > > 2. Making a 3T atlas representative target. I can make the target using > your data. > However, it is up to the FreeSurfer developers to decide how to proceed. > Adding the control structures to enable use of input-dependent or > user-selectable > atlas representative target amounts to a revision. > The FreeSurfer developers may or may not wish to undertake such > a revision. In any case, it can't happen tomorrow. > > Avi > ----------------------------------------------------------------------- > >Date: Tue, 21 Apr 2009 12:52:45 +0800 > >Subject: Re: [Freesurfer] t4_read error (fwd) > >From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > >To: Avi Snyder <avi(a)npg.wustl.edu> > >Cc: freesurfer(a)nmr.mgh.harvard.edu, fischl(a)nmr.mgh.harvard.edu, > nicks(a)nmr.mgh.harvard.edu > > > > Hi avi: > > > >Thanks for your help. Still have two questions. > > > >1) How to determine whether the Talairach transform is reasonable > >based on recon-all.log? > > > >2) As you mentioned, we can make a suitable 3T atlas-representative > >target to resolve the Talairach transform problem. Now, we have several > >dozens of adult Chinese 3T MPRAGE data. Would you please give us some cues > >how to generate the 3T atlas target with FreeSurfer? > > > > Anyone has ideas on this issue,please let me know. > > > >Thanks again. > > > >Zonglei > > > >2009/4/20 Avi Snyder <avi(a)npg.wustl.edu> > > > >> Zonglei, > >> > >> The log files contain the string "t4_read:..... read error" > >> This is a benign message indicating the the affine transform > >> file was not found. This always occurs at the start of the > >> affine transform sequence and carries no significance. > >> > >> Review of the log file indicates that in the case of subjA39 > >> Talairach atlas transform achieved a reasonable numeric result. > >> > >> In the case of subjA06 the Talairach transform did not achieve > >> a good result. This is an algorithmic issue. It appears that > >> the talairah_avi module was initiated twice, I assume, in an attmept > >> to improve the result, but the result did not improve. In this > >> log file the "read error" message occurs twice but it simply > >> means that the transform sequence was initiated twice. > >> > >> So, there is a problem but the the "read error" message has nothing > >> to do with it. Poor MP-RAGE to atlas representative target results > >> most likely are attributable to use of a 1.5T target with 3T input. > >> It this is correct, then a permanent solution to the problem could > >> be achieved by selecting the > >> atlas-representative target according to the MP-RAGE source. > >> Generation of a suitable 3T target would not be difficult. > >> > >> Avi > >> ------------------------------------------------------ > >> Date: Sun, 19 Apr 2009 22:52:35 +0800 > >> Subject: Re: [Freesurfer] t4_read error (fwd) > >> From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > >> To: Avi Snyder <avi(a)npg.wustl.edu> > >> Cc: fischl(a)nmr.mgh.harvard.edu, nicks(a)nmr.mgh.harvard.edu, > >> freesurfer(a)nmr.mgh.harvard.edu > >> > >> Hi avi: > >> > >> Thanks for your response, attachments are my recon-all.logs. > >> If you have any ideas,please let me know. > >> > >> Thanks again. > >> > >> 2009/4/17 Avi Snyder <avi(a)npg.wustl.edu> > >> ----------------------------------------------- > >> > Zonglei, > >> > > >> > Send the log file to > >> > > >> > avi(a)npg.wustl.edu > >> > ---------------------------------------- > >> > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) > >> > >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> > >To: Avi Snyder <avi(a)npg.wustl.edu> > >> > >cc: nicks(a)nmr.mgh.harvard.edu > >> > > > >> > >do you want to contact him directly? > >> > > > >> > >On Fri, 17 Apr 2009, Avi Snyder wrote: > >> > > > >> > >> Most likely the MPRAGE->atlas computation aborted without creating > >> > >> the relevant t4 file (ASCII representation of the affine > transform). > >> > >> This could occur if the images were somehow corrupted. > >> > >> > >> > >> Alternatively, the t4 file is present but a recent OS upgrade has > >> caused > >> > >> the previously compiled t4_read FORTRAN function to bomb. I have > seen > >> this > >> case > >> > >> once before and have therefore created an all-C t4 i/o module. > >> > >> > >> > >> We can distinguish these cases by asking if you got a core dump, of > if > >> > >> a t4 file is still present. The complete tal transform log file > would > >> > >> be diagnostically very helpful. > >> > >> > >> > >> Avi > >> > >> ------------------------------------------ > >> > >>> Date: Fri, 17 Apr 2009 07:58:36 -0400 (EDT) > >> > >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> > >>> To: Avi Snyder <avi(a)npg.wustl.edu> > >> > >>> cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > >> > >>> Subject: [Freesurfer] t4_read error (fwd) > >> > >>> > >> > >>> Hi Avi, > >> > >>> > >> > >>> do you know what this message means? > >> > >>> > >> > >>> thanks > >> > >>> Bruce > >> > >>> ---------- Forwarded message ---------- > >> > >>> Date: Fri, 17 Apr 2009 19:32:05 +0800 > >> > >>> From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > >> > >>> To: freesurfer(a)nmr.mgh.harvard.edu > >> > >>> Subject: [Freesurfer] t4_read error > >> > >>> > >> > >>> Dear all: > >> > >>> Recon-all has finished without error in my reconstruction. > However, > >> when I > >> > >>> checked recon-all.log, I found three was a error “t4_read: > >> > >>> talsrcimg_to_711-2C_as_mni_average_305_t4 read error”. > >> > >>> > >> > >>> What's this error mean? Does it have some effects on my > >> reconstruction? > >> > >>> > >> > >>> Thanks > >> > >>> > >> > >>> -- > >> > >>> Zonglei Zhen, PhD > >> > >>> Assistant Professor of Cognitive Neuroscience > >> > >>> BNU Imaging Center for Brain Research, State Key Laboratory of > >> > Cognitive > >> > >>> Neuroscience and Learning, P.R. China > >> -- > >> Zonglei Zhen, PhD > >> Assistant Professor of Cognitive Neuroscience > >> BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive > >> Neuroscience and Learning, P.R. China > > > >-- > >Zonglei Zhen, PhD > >Assistant Professor of Cognitive Neuroscience > >BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive > >Neuroscience and Learning, P.R. China > > BEGIN {go = 0;} > > (NF == 6 && go > 0) { > for (i = 1; i <= 6; i++) p[k++] = $i; > go++; if (go == 3) {go = 0;} > } > > /eta,q/ {p[k++] = $2;} > > /second partial in parameter space/ {go++; k = 0;} > > END { > for (k = 0; k < 12; k++) printf ("%5.0f", p[k]); > printf ("%10.5f\n", p[12]); > } > > -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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ROIs of BV not coinciding with FS
by Barnali Basu 22 Apr '09

22 Apr '09

Hello Thanks for your previous responses. Those have been helpful. I have been trying to use some ROIs generated in BrainVoyager(BV). I have converted the ROI text file of BV to Freesurfer label text file format, using a small perl script (attached as testperl.txt). I am also attaching the original BV ROI file and the changed FS label file for your reference. My method seemed to work( no error), however all the ROIs , regardless of where they should be ( like frontal, MT etc) are landing up on the occipital area, including the occipital ROI itself. The BV ROI data sent to me was generated in Tal space, also, I have done manual Talairaching to the same data in FS using tkregister2. So I assume both versions of the subject (BV and FS) are in same space. Am I right? It would be great if you could suggest me where I must be going wrong. FYI, the BV processing has been done on a windows machine and sent to me. I work only on FS on Ubuntu. I am also attaching pictures of frontal and an occipital ROI on the inflated brain. Looking forward to some help. -- Barnali Basu Cell : 425 638 2936 Home: 206 257 0174

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qdec versions for .Qdecrc
by raka maitra 22 Apr '09

22 Apr '09

Hello I am using Freesurfer v 4.1.0 I would like to have the advantage of the updated qdec of v 4.2 or 4.3 for my data. Specifically, I would like to use the 'MEASURE# = some_measure' modification for .Qdecrc Is it advisable to replace the qdec, qdec_glmfit and qdec.bin (from freesurfer/bin) in the 4.1 version with that of 4.2. or 4.3 ? Will that be sufficient ? Thanks in advance Raka

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ventricles labeled as white matter in hydrocephalus brain
by Dana W. Moore 22 Apr '09

22 Apr '09

I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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3d reconstruction of the hippocampus or thalamus
by asaf achiron 22 Apr '09

22 Apr '09

hi group, Is there a way to reconstruct in 3d the hippocampus or thalamus segmentation in Freesurfer? this is for verification of the automatic process, thank you Asaf

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Using a Label with Volume-based Monte Carlos
by Dave Brohawn 22 Apr '09

22 Apr '09

Hello, Here is my bugr information. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090416 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd /autofs/space/ventzl_016/users I am curious if it is possible to run a monte carlo analysis using volume data including a label file I generated. Here is the command I tried to run: mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --C $SUBJECTS_DIR/fsgd/All-18.mat --label $SUBJECTS_DIR/fsaverage/label/subcortical.label --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/All18Vol_MCSIM1 --fwhm 13.37 This would be the first of ten monte carlo simulation commands. It returned an error message saying: gdfReadHeader: reading /autofs/space/ventzl_016/users//fsgd/All-18.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 CC 2 T INFO: gd2mtx_method is dods simbase /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/All18Vol_MCSIM1 ERROR: need --surf with --label The subcortical label I generated from the "aseg" segmentation overlay for fsaverage includes the left and right segmentations of the following regions: Amygdala, hippocampus, DC, Putamen, Accumbens, Pallidum, Thalamus Proper, and Caudate. The brain stem label is also included. Please let me know if running a monte carlo for volume with a label is possible. Thank you, Dave Brohawn

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discrepancy with mris_glmfit-sim annotation
by Devdutta W 22 Apr '09

22 Apr '09

Hi, While going through the annotation of the clusters, we noticed that the regions that the cluster summary prints out do not correspond to the actual location in the brain. For example, in the summary one of the clusters is reported to be in the isthmus of cingulate. However, when I look at the corresponding cluster on tksurfer it is quite clearly not medial (in fact it is on the temporal lobe). Has anybody encountered this problem before? If so, any idea why this is happening and how it can be fixed? I appreciate any help in this matter. Regards, Devdutta

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spherical template: CMA training set
by Juranek, Jenifer 22 Apr '09

22 Apr '09

Is any information about the manually-parcellated (CMA) training set used to create the spherical template used in fsv4.*? The information reported in Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing study. Does this sound about right? Or have there been any updates to the spherical template since then? Many Thanks for any info, Jenifer

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Freesurfer April 2009