Freesurfer

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30132 discussions

label value 0 in annot file
by Forrest Sheng Bao 31 Jul '11

31 Jul '11

hi, I noticed an interesting thing today. I used read_annotation function in matlab to load an .annot file, i.e., [Vertexes,Label,Colortable]=read_annotation(AnnotFile); But some labels in Labels were 0's. They did not appear in the 5th column of Colortable.table. And 0 was the only label that i couldn't find in the 5th column of Colortable.table. All other labels were fine. Any idea what the cause of 0's as labels might be? Cheers, Forrest

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mri_robust_register registration file
by Kami Koldewyn 29 Jul '11

29 Jul '11

Hi All, I was trying to use the registration file that is created by mri_robust_register with mri_vol2vol - but it is in a different format than registration files created by bbregister or tkregister. Is it fsl format? Is there an easy way to use this registration file with other freesurfer functions (like mri_vol2vol)? Thanks very much, -kami --------------------------------------------------------------- Kami Koldewyn, PhD. McGovern Institute for Brain Research MIT, Building 46 Room 4141 (Kanwisher Lab) Cambridge, MA 02139 kamik(a)mit.edu

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Intensity Normalization error
by Antonella Kis 29 Jul '11

29 Jul '11

Dear Bruce, 1). What is the minimum value/the range for the intensity in order to be considered acceptable? I know the value in wm should be very close to 110 but what is the accepted value closed to this? If is not exactly 110 (foe example if is 101) do I need to add control points in order to normalize the intensity and get the value 110? 2). I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') I Why I don't have an option for the no. of vertices? Can I get a table with both data: cortical thickness and no. of vertices? Many thanks, Antonella

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Problems at mri_em_register
by Tali Swisher 29 Jul '11

29 Jul '11

Hi all, I'm running FreeSurfer v4.0.5 and keep getting the following error: ####################################### #------------------------------------- #@# EM Registration Thu Jul 28 16:09:51 EDT 2011 /home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.0 using (130, 118, 99) as brain centroid... mean wm in atlas = 107, using box (130,93,92) --> (129, 143,105) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux compute-4-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011 Any ideas? Thanks! -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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trac-all -path errors
by Ping-Hong Yeh 29 Jul '11

29 Jul '11

Hi, I got the error running "trac-all -path -c configure.txt" ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt I can only find only image files in the "dlabel/diff" directory, but not text files. Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? Thanks, Ping

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mris_expand not expanding
by Reza Farivar 29 Jul '11

29 Jul '11

Hello, I've tried running mris_expand on several different surfaces, with or without the -thickness flag, and while it ends without error and creates the output file, the output looks identical to the input. I've tried even expanding by large amounts, large percentages of thickness values, but without luck. Are there some hidden flags that I should be using? Thanks, Reza

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Re: [Freesurfer] 20% changes
by Bruce Fischl 29 Jul '11

29 Jul '11

Ji Jessica, that's pretty low contrast. I would also bet that it's low bandwidth and hence you have big temporal lobe B0 distortions that will change with subject positioning. Are you stuck with this data going forward, or can you change the acquisition parameters? If not, I think you will have to live with lower reliability and sensitivity cheers Bruce On Thu, 28 Jul 2011, Jessica Liu wrote: > Hi Bruce, > > I was thinking it could be quality as well, since I asked about that in a previous question where my group compared 3T and 1.5T data from the > same subject. Unfortunately we only obtained 1 scan for all of our subjects and nearly all of our data is from a 1.5T scanner. I've attached > coronal, axial, and sagittal views with aseg+aparc, and one image without aseg+aparc for a WM segmentation check. Thanks for your help! > > Jessica > > On Thu, Jul 28, 2011 at 11:39 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Jessica > > the problem may be data quality! At 1.5T with a volume coil we would typically get 2 scans to average. A TR of 14 is pretty short > and will reduce the SNR, and a TE of 6 is quite long and will reduce contrast. Can you send us a tif of one slice to look at? > > Bruce > > > On Thu, 28 Jul 2011, Jessica Liu wrote: > > Hi Martin, > > When I did longitudinal analyses in the past, the output was very strange even though I think I did everything correctly. If > it's not too > much trouble for you, could you please take a look at my data and tell me what I've done wrong? Since the files are so > large, how would I > send over my data? Also, I'm using is a head coil 1.5T single-channel GE scanner. The sequence I'm using is 3D SPGR with TR > = 14 msec, TE = > 6.2 msec, TI = 450.0, FOV 24 cm, data acquisition matrix = 256x192, and 124 slices with 1.6 mm thickness. Your help is truly > appreciated! > > Jessica > > On Thu, Jul 28, 2011 at 7:37 AM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Jessica, > > I'd recommend to run the -base and the -long on these and see what > happens. If you then still see these differences, maybe we can take a > look at your data to figure out what causes this. It could be that the > WM segmentation fails somewhere. Anyway, the longitudinal stream should > help fix these things. > > Are these mprages or multi echo mprages? 3T? what coil? > > Best, Martin > > On Wed, 2011-07-27 at 18:01 -0700, Jessica Liu wrote: > > Hi Bruce, > > > > Well for one of the subjects, the total temporal lobe volume from the > > first scan was 149937 mm3, and the second scan's total temporal lobe > > volume was 183121 mm3. These numbers were found by summing the > > volumes from the entorhinal, fusiform, parahippocampal, temporal pole, > > transverse temporal, and the inferior, middle, and superior temporal > > sections found in the lh.aparc.stats, rh.aparc.stats, and wmparc.stats > > for the respective scans. Hippocampus volumes were found by summing > > the right and left parts found in aseg.stats. > > > > Jessica > > > > On Wed, Jul 27, 2011 at 5:37 PM, Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu> wrote: > > how are you computing the 20% difference? We definitely don't > > see this, and Martin has done extensive testing of > > repeatability. > > Bruce > > > > > > > > On Wed, 27 Jul 2011, Jessica Liu wrote: > > > > Hi Martin, > > > > Thanks for getting back to me. Actually I have two > > young controls who have 20% differences between two > > scans a day apart. Visually, there > > are not abnormalities for the surfaces and hippocampus > > in both subjects i.e. on tkmedit, the color of the > > hippocampus area (yellow) looks > > alright to me. I don't see any motion artifacts > > either. > > > > Jessica > > > > On Wed, Jul 27, 2011 at 12:15 PM, Martin Reuter > > <mreuter(a)nmr.mgh.harvard.edu> wrote: > > Hi Jessica, > > > > I don't think this is normal. Is this a single > > subject? Of course in a > > single subject lots of stuff can go wrong. Are > > the surfaces correct? And > > the hippo label? Are there motion artifacts in > > the image etc. > > > > Anyway, you should process this with the > > longitudinal stream: > > > > http://freesurfer.net/fswiki/LongitudinalProcessing > > which should increase repeatability. > > > > Best, Martin > > > > > > On Wed, 2011-07-27 at 09:01 -0700, Jessica Liu wrote: > > > Hi, > > > > > > We found 20% differences in temporal lobe brain > > volume and ca. 5% > > > difference in the hippocampus volume between two > > data sets of a young > > > normal volunteer scanned 2 days apart. > > > > > > We use the one-step 19 hours recon-all -all > > procedure and directly sum > > > select values taken from the lh.aparc.stats, > > rh.aparc.stats, and > > > wmparc.stats. The values summed were based on > > information given from > > > > > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-April/005000.html > > > > > > My question is, are these observations normal for > > Freesurfer? Any > > > comments are greatly appreciated. Thanks! > > > -- > > > Pom & Jessica > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The information in this e-mail is intended only for > > the person to whom it is > > addressed. If you believe this e-mail was sent to you > > in error and the e-mail > > contains patient information, please contact the > > Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail > > was sent to you in error > > but does not contain patient information, please > > contact the sender and properly > > dispose of the e-mail. > > > > > > > > > > > > > >

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Re: [Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction
by Douglas N Greve 29 Jul '11

29 Jul '11

Yes, that should work. You will need a registration matrix to give to mri_compute_volume_fractions. You can get this from tkregister2: tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat when you run this, hit the compare button to make sure that the mrs box falls on the part of the anatomical you think it should be. Then hit "Save" to save the registration. doug _andreia_(a)sapo.pt wrote: > Hi Doug, > > This already sheds some light on the issue! I didn't know > mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have > the anatomical and the MRS data acquired in the same session, so I > won't need the EPI. If I manage to create the MRS volume using the > header info and mri_volsynth I only need to coregister my anatomical > with the synthetised volume and then run mri_compute_volume_fractions > through the synthesed volume and the identity matrix (?) (since my > data are from the same session) to get the % of the different tissue > types only inside the voxel. Of course I'll need more advice on this > later, but one thing at a time. > > Thanks! > Andreia > > > > Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Sorry, I don't know anyone who can help with that. As you note, people >> do it, so there must be people around who can extract the relevant >> information out of the header. The information you need are the >> direction cosines and RAS of the corner of the voxel. You can feed this >> into mri_volsynth. >> >> To register to FS, you'll need to have a whole-brain volume collected >> during the same session. If you collected the anatomical analyzed in FS >> at the same time, then you don't need another. If you did not, you can >> literally use any whole brain acquisition, eg, a single TR of an EPI >> (less than 10 sec to acquire). You can then register the EPI to the >> anatomical with bbregister. This gives you a "register.dat". You can >> then concatenate that with the EPI-MRS registration (I can show you >> how). After that, you can run mri_compute_volume_fractions passing it >> the synthesized volume and the register.dat (or identity matrix if same >> session). >> >> Another alternative is to collect an actual MRI volume that spans your >> MRS volume. You can then substitute that for the synthetic volume. Note >> that the actual pixel content of this volume is irrelevant -- it's just >> used to get geometry information out of it. This will be the easiest if >> you can do it. >> >> doug >> >> _andreia_(a)sapo.pt wrote: >>> Hi Doug, >>> >>> Do you know who can help me with this? That's exactly what I think >>> that I need to do... The thing is that, unfortunately, I can't find >>> anyone who can describe how the creation of an MRI "volume" from the >>> MRS voxel is done, although this approach is present in many many >>> papers. >>> >>> About the second part, how do I register the synthetized MRI "volume" >>> to the FS anatomical? And how can I get the volumes of only that >>> "volume"? >>> >>> (Hopefully I'll find a way to do the first part...) >>> >>> Thanks, >>> Andreia >>> >>> >>> >>> >>> Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Andreia, I've done this before using information in the >>>> spectroscopy >>>> header, then synthesizing an MRI "volume" with one voxel that >>>> covers the >>>> size of your spectroscopy voxel, then registering that to the FS >>>> anatomical, then computing the partial volume fractions from the >>>> anatomical. The hard part is the first step, which I can't really >>>> advise >>>> you on. >>>> >>>> doug >>>> >>>> _andreia_(a)sapo.pt wrote: >>>>> Dear list, >>>>> >>>>> I am performing single-voxel and multivoxel spectroscopy analysis and >>>>> I need to do partial volume correction. I found a thread on the list >>>>> of someone asking if it possible to achieve this using Freesurfer >>>>> (see >>>>> below), but there is no answer saying how it is done. My question is >>>>> how can I define the voxel (for single-voxel) and the chosen voxels >>>>> (for multivoxel) in the anatomical data set to use the >>>>> segmentation of >>>>> only that defined voxel? I'm using a Siemens TrioTim 3T. All >>>>> acquisitions are in the same session. The anatomical dataset is an >>>>> average of 2 MPRAGEs which I've already processed using FS, and the >>>>> spectra files are .rda. The header of the MRS data has info on >>>>> vectors, but I don't know how to use them. >>>>> >>>>> >>>>> >>>>> "Re: [Freesurfer] need info for beginner >>>>> >>>>> Bruce Fischl >>>>> Thu, 26 Apr 2007 11:17:01 -0700 >>>>> >>>>> Hi Pom, >>>>> >>>>> yes, people here are using it for spectroscopy and for partial volume >>>>> correction (also for voxel placement). >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote: >>>>> >>>>> Hi, >>>>> >>>>> I am about to install FREE SURFER for my Spectroscopy work. >>>>> I want to use the software to perform GM/WM segmentation on my >>>>> single voxel data sets. >>>>> >>>>> I am wondering if any one on this mailing list is currently >>>>> doing this task. I would like to get comments. >>>>> >>>>> My study is on a GE 3T scanner. >>>>> >>>>> thank you, >>>>> >>>>> Pom" >>>>> >>>>> >>>>> >>>>> Any advice, please? >>>>> >>>>> Thank you! >>>>> >>>>> Andreia >>>>> >>>>> >>>>> -- >>>>> >>>>> Andreia Pereira, MSc student >>>>> Visual Neuroscience Laboratory >>>>> IBILI-Faculdade de Medicina >>>>> Azinhaga de Santa Comba >>>>> 3000-354 Coimbra Portugal >>>>> Phone +(351) 239480220 >>>>> Fax +(351) 239480280 >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>> you in error >>>> but does not contain patient information, please contact the sender >>>> and properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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script to calculate global cortical thickness, volume etc, Is there any better way
by Knut J Bjuland 29 Jul '11

29 Jul '11

Dear Sir/Madame I have written a script that calculates the cortical thickness for the whole hemisphere of the brain. I have some question if there are any ways to improve the script. I can quite easily write a script in Python that runs through the file I have created and append it to a coma separate file. What is the standard way to get average cortical thickness for the entire brain using ?h.cortex.label for serval different subjects? Your faithfully Knut J #!/bin/sh subjects="" for filename in ${subjects}; do echo "subject ${filename}" mris_anatomical_stats -f rh_${filename}.txt ${filename} rh mris_anatomical_stats -f lh_${filename}.txt ${filename} lh done

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20% changes
by Jessica Liu 28 Jul '11

28 Jul '11

Hi, We found 20% differences in temporal lobe brain volume and ca. 5% difference in the hippocampus volume between two data sets of a young normal volunteer scanned 2 days apart. We use the one-step 19 hours recon-all -all procedure and directly sum select values taken from the lh.aparc.stats, rh.aparc.stats, and wmparc.stats. The values summed were based on information given from https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-April/005000.html My question is, are these observations normal for Freesurfer? Any comments are greatly appreciated. Thanks! -- Pom & Jessica

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