Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

re-running recon-all failing
by Satrajit Ghosh 20 Jul '11

20 Jul '11

hi all, i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting the following error on all the subjects. simply executing recon-all -s subjid -all any ideas? cheers, satra ---------- unfolding failed - restoring original position -------------------- 0750: dt=0.001250, rms=0.380 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 4 hours, 1 minutes and 50 seconds. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Mon Jul 18 14:54:53 EDT 2011 /g2/users/satra/TESTCVS/surfaces/ek041bk/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse ERROR: mri_ca_register with non-zero status 0

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tksurfer image rendering error
by Martina Ly 20 Jul '11

20 Jul '11

Hello freesurfer community, I am viewing an inflated image generated by tksurfer using the command: tksurfer "subjid" rh inflated The image appears to have rendering issues only on certain workstations (Mac OS X 10.6.5) but works on other linux machines. The shading doesn't have high resolution (low resolution gradients, appears to be 8bit). I've attached a photo. I am accessing the data locally and the video card driver (ATI) has been updated. I've also tried entering: export doublebufferflag=1. Any help or suggestions would be greatly appreciated! Best, Martina

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ROI analysis with label in both hemispheres
by Katie Bettencourt 20 Jul '11

20 Jul '11

Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie

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Multiecho sequences available for Siemens
by Brian C. Schweinsburg, Ph.D. 20 Jul '11

20 Jul '11

Hi Folks, I noticed in the multiecho portion of the freesurfer wiki that it says custom multiecho sequences are available from Martinos for use. I was wondering who I might contact for information on obtaining sequences for our 3T Siemens scanner as I hoped to test these out with freesurfer. Thanks, Brian

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Contrast with two covariates in conjunction?
by Gonzalo Sanchez Benavides 20 Jul '11

20 Jul '11

Dear Freesurfers, I'm exploring the relationship among cortical thickness, aging and some cognitive variables in a sample of healthy elders, and I want to test this relationship regardless sex and years of education. I think is easy to make contrasts to explore separately the correlation between age (or a cognitive measure) and thickness. However I am wondering if its possible to know the areas in which both correlations coincide. Does it make sense to use a contrast like this for such purpose? 0 0 0.5 0.5 0 0 0.5 0.5 sex age edu cognitive measure Many thanks in advance for your answer -- Gonzalo Sánchez Benavides

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stats files query
by Rebecca McCourt 20 Jul '11

20 Jul '11

Hi, I see that some stats files are more reliable than others for certain types of data, for instance I read that aseg isn't that reliable for WM/GM. Which files I should use to find cortical thickness (whole-brain and each hemisphere), GM/WM volumes (cortical) and whole brain volume? What's the difference between mris_anatomical_stats and mri_segstats, and which of these should I use to get the data specified above? Thanks in advance for your help, Rebecca M

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Calculate WM, GM and CSF volume
by Fellhauer, Iven 20 Jul '11

20 Jul '11

Dear All, I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta -calabel -segstatts -subject <subject> Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? Best regards, Iven Fellhauer

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mgz to nii.gz... T1 and ROIs. Is there a way to do (5) from command line?
by r.navarra＠itab.unich.it 20 Jul '11

20 Jul '11

Hi FS expert. I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same for many subjects. The issue's about dimensions. When I use fslview, it respond me that "All overlays must have same dimensions as the base image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are differents dimensions and 0.5mm3 voxel size. To work now I use this pipeline: ( command line :) ) 1) mri_convert ---> nii 2) gzip ---> nii.gz 3) fslmaths t1 -sub t1 t1_zero 4) mricron t1_zero -l 0 -h 100 -o roi1.nii.gz ( GUI only :( ) 5) (from mricron) save as nifti roi1_ok.nii.gz Is there a way to do (5) from command line? Thanx Riccardo

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finding closest vertex in matlab
by Corey Keller 19 Jul '11

19 Jul '11

Hi Freesurfers, I have talairach coordinates of electrodes sitting on the brain. I am hoping to use the Desikan-Killiany parcellation scheme to determine which cortical region each electrode lies closest to in standard space. I am using read_annotation in matlab to read the lh.aparc.annot file and find the vertices associated with each label. I am wondering how to determine which label each electrode lies closest to? Is there a TAL or RAS to vertex function in matlab? Thanks. Best, Corey

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Re: [Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction
by Douglas N Greve 19 Jul '11

19 Jul '11

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

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