Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

RE: [Freesurfer] Faster and Parallel recon-all
by Goradia, Dhruman D 22 Mar '06

22 Mar '06

Hi Daniel, The script is ok but it still does not make it to the end. As the script is designed to send me an email at the end of the last step, I got an email within 15 min after I executed the script saying that "recon-all 14777 finished with errors at Tue Mar 21 18:46:15 EST 2006". However it went on the complete the "gcareg" step. I have attached the status and log files for your reference. If you get a chance have a look at it. I believe this problem is not due to super-recon script but due to recon-all script. Please let me know. I am very interested in the super-recon script, as it takes about 30 hrs to process 1 scan currently. -Dhruman -----Original Message----- From: Daniel Goldenholz [mailto:daniel@nmr.mgh.harvard.edu] Sent: Tuesday 21 March 2006 17:09 To: Goradia, Dhruman D Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman Thanks for catching that. Spelling was never my strong point. I have corrected the script on my website. As for you second problem, did you properly remove the waitfor step1-00.done from the motion correction step, since you say you skipped step1-00, i.e. the invol step? I mention this in a comment near the top of the script. D Goradia, Dhruman D wrote: >Hi Daniel, >I was having a second look at the script and apparently the script is >fine with a small spelling error. The STAT variable which is set at 3 >different instances has spelling error in "scripts" where "t" is >missing. >Once this was corrected the script is fine but it's still not working. >It initiates all the processes and then just sits idle. After waiting >for half an hour it still does not make step1-00.done (I start directly >with motion cor) keeping all the other processes waiting. I am still >probing into this. If you can think of something that might be of help >then let me know. >-Dhruman > >-----Original Message----- >From: Daniel Goldenholz [mailto:danielg@bu.edu] >Sent: Tuesday 21 March 2006 11:25 >To: Goradia, Dhruman D >Subject: Re: [Freesurfer] Faster and Parallel recon-all > >Dhruman > >That's confusing. I think you should take one line of executable code >from your script that produces that behavior and then email it to the >freesurfer list. > >It sounds to me like the recon-all script ASSUMES that the log file >exists if you specify a name. I thought it actually creates one first, >but I could have been mistaken there, and if so I will need to add a few > >extra lines of code. >PLEASE follow up on this. It will help others. > >The other thing to try is to create a text file first, such as like >this: >echo "#Starting recon-all manually..." > >/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log > >and then see if my script is ok. > >Keep me posted. > >D > >Goradia, Dhruman D wrote: > > > >>Hi Daniel, >>I tried to use the script super-recon on mac OX S using bash shell. I >>made the necessary changes to make it operable in bash. However when I >>run the script its gives me the following error: >> >>Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.l o >> >> >g > > >>:not a file or directory. >> >>I tried to run the first 3 steps of the script (motioncor, >>nuintensitycor, talairach) and it gives the above error. However if I >>remove the log and status flags, the first 3 steps executes properly. >> >> >Do > > >>you have any idea why? Do you see any problem if I delete the log and >>status flags from the whole script and use it? >>-Dhruman >> >>-----Original Message----- >>From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel >>Goldenholz >>Sent: Thursday 16 March 2006 15:17 >>Cc: Freesurfer Mailing List; Nick Schmansky >>Subject: Re: [Freesurfer] Faster and Parallel recon-all >> >>Ah. Silly me, I didn't notice the -log and -status options. Thanks >> >> >Nick. > > >>I have now included those into my super-recon script as well. Problem >>solved. >> >>(if you have seen my script already, you may need to hit RELOAD on your >> >> > > > >>browser to see the new version) >>Daniel >> >> >> >> >> >>>Nick Schmansky wrote: >>> >>> >>> >>> >>> >>>>The script looks good. The one thing it needs though is for the >>>> >>>> >>>> >>>> >>right >> >> >> >> >>>>and left hemi steps to log to separate files, otherwise output to >>>> >>>> >>>> >>>> >>recon- >> >> >> >> >>>>all.log will be interleaved, making debugging impossible. >>>> >>>>On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: >>>> >>>> >>>> >>>> >>>> >>>> >>>>>Ooops. I sent the below with the wrong subject tag. Here it is >>>>> >>>>> >>>>> >>>>> >>again: >> >> >> >> >>>>>Daniel Goldenholz wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Freesurfers >>>>>> >>>>>>I was hoping someone else would do this, but well, it seems that no >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>one did. So I went ahead and made this myself. >>>>>>Amusingly, I don't NEED to reconstruct any brains right now, so I >>>>>>don't have anything to test this out with. >>>>>>Please someone try it, and let me know if it is helpful. >>>>>> >>>>>>What I did was write a script that runs each and every part of the >>>>>>recon-all -all stream, one command at a time. (based on the NEW >>>>>>version 3 stream). >>>>>>Each one is loaded with -waitfor and -notify so that the dependency >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>structure is intact. >>>>>>However, ALL of the commands start running in the background! If >>>>>>you have a 2 more processor system, then recon-all should complete >>>>>>in about HALF the time as it usually does, since all the hemisphere >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>specific stuff can be done in parallel. >>>>>>At the completion of each hemipshere, it will email you. >>>>>> >>>>>>I included a command for each minute step so that people can easily >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>fiddle with options and commands and so forth. >>>>>> >>>>>>Obviously, if you run recon-all -autoreon1, then you can then run >>>>>>my script (after deleting the step1-??.done lines). >>>>>>If you run recon-all -autorecon2, then you can run my script (after >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>deleting the step1-??.done and step2-??.done lines) >>>>>>And so forth. >>>>>> >>>>>>To see the script, go here: >>>>>>http://www.nmr.mgh.harvard.edu/~daniel >>>>>>click on fMRI scripts >>>>>>click on super-recon >>>>>> >>>>>>Enjoy, and PLEASE email me if you use this. If there are >>>>>>corrections I can easily post them. >>>>>>Daniel >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Using overlay in Freesurfer
by Salil Soman 22 Mar '06

22 Mar '06

Can the overlay feature in freesurfer be used to overlay anatomic images? (or does the overlay image have to be spatial data). I'm trying to overlay a EPI image over a T1 image, and the EPI volume is showing up as a yellow block. The EPI and the T1 mgz files were both generated by mri_convert from spm files. Thanks, Salil Soman sal(a)bwh.harvard.edu

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asegs
by Rahul Desikan 22 Mar '06

22 Mar '06

Hi, Has anyone noticed the previously reported problem with mri_ca_register in the stable version? I have been using the stable version of the binaries and have not been able to sucessfully generate asegs. The script I use to generate the aseg.mgz file is: /space/krupa/7/users/rahul/ppg/recons/scripts/aseg_rerun.csh I have noticed all of my jobs on seychelles fail with a 'Segmentation fault' error message: blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0Segmentation fault All the jobs fail at the same location with the same error message (check ~rahul/.pbsrc/pbsjob_2675* for an example). Does anyone have any ideas about this? thanks, rahul --

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RE: [Freesurfer] Faster and Parallel recon-all
by Goradia, Dhruman D 21 Mar '06

21 Mar '06

Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in "scripts" where "t" is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman -----Original Message----- From: Daniel Goldenholz [mailto:danielg@bu.edu] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman That's confusing. I think you should take one line of executable code from your script that produces that behavior and then email it to the freesurfer list. It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a few extra lines of code. PLEASE follow up on this. It will help others. The other thing to try is to create a text file first, such as like this: echo "#Starting recon-all manually..." > /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log and then see if my script is ok. Keep me posted. D Goradia, Dhruman D wrote: >Hi Daniel, >I tried to use the script super-recon on mac OX S using bash shell. I >made the necessary changes to make it operable in bash. However when I >run the script its gives me the following error: > >Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.lo g >:not a file or directory. > >I tried to run the first 3 steps of the script (motioncor, >nuintensitycor, talairach) and it gives the above error. However if I >remove the log and status flags, the first 3 steps executes properly. Do >you have any idea why? Do you see any problem if I delete the log and >status flags from the whole script and use it? >-Dhruman > >-----Original Message----- >From: freesurfer-bounces(a)nmr.mgh.harvard.edu >[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel >Goldenholz >Sent: Thursday 16 March 2006 15:17 >Cc: Freesurfer Mailing List; Nick Schmansky >Subject: Re: [Freesurfer] Faster and Parallel recon-all > >Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick. > >I have now included those into my super-recon script as well. Problem >solved. > >(if you have seen my script already, you may need to hit RELOAD on your >browser to see the new version) >Daniel > > > >>Nick Schmansky wrote: >> >> >> >>>The script looks good. The one thing it needs though is for the >>> >>> >right > > >>>and left hemi steps to log to separate files, otherwise output to >>> >>> >recon- > > >>>all.log will be interleaved, making debugging impossible. >>> >>>On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: >>> >>> >>> >>> >>>>Ooops. I sent the below with the wrong subject tag. Here it is >>>> >>>> >again: > > >>>>Daniel Goldenholz wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Freesurfers >>>>> >>>>>I was hoping someone else would do this, but well, it seems that no >>>>> >>>>> > > > >>>>>one did. So I went ahead and made this myself. >>>>>Amusingly, I don't NEED to reconstruct any brains right now, so I >>>>>don't have anything to test this out with. >>>>>Please someone try it, and let me know if it is helpful. >>>>> >>>>>What I did was write a script that runs each and every part of the >>>>>recon-all -all stream, one command at a time. (based on the NEW >>>>>version 3 stream). >>>>>Each one is loaded with -waitfor and -notify so that the dependency >>>>> >>>>> > > > >>>>>structure is intact. >>>>>However, ALL of the commands start running in the background! If >>>>>you have a 2 more processor system, then recon-all should complete >>>>>in about HALF the time as it usually does, since all the hemisphere >>>>> >>>>> > > > >>>>>specific stuff can be done in parallel. >>>>>At the completion of each hemipshere, it will email you. >>>>> >>>>>I included a command for each minute step so that people can easily >>>>> >>>>> > > > >>>>>fiddle with options and commands and so forth. >>>>> >>>>>Obviously, if you run recon-all -autoreon1, then you can then run >>>>>my script (after deleting the step1-??.done lines). >>>>>If you run recon-all -autorecon2, then you can run my script (after >>>>> >>>>> > > > >>>>>deleting the step1-??.done and step2-??.done lines) >>>>>And so forth. >>>>> >>>>>To see the script, go here: >>>>>http://www.nmr.mgh.harvard.edu/~daniel >>>>>click on fMRI scripts >>>>>click on super-recon >>>>> >>>>>Enjoy, and PLEASE email me if you use this. If there are >>>>>corrections I can easily post them. >>>>>Daniel >>>>> >>>>> >>>>> >>>>> > > >

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total intracranial volume question
by Eli Diamond 21 Mar '06

21 Mar '06

Hello, I'm writing because I am trying out some structure-function analyses and I would like to normalize my label volume measurements with the total intracranial volume. I was informed that this value is in <subject>/stats/aseg.stats. I was surprised at the range of TIVs that I saw in my 29 subjects (from 1400cm^3 to 2500cm^3). so I looked up what the normative values are for TIV, and it appears that the TIVs estimated for my group are irregular given the standard mean TIV and normal variance. (from one paper that I looked at it seems like the avereage TIV is around 1500cm^3 and that typical variation is measured in the 10-100cm^3 range, not an order of magnitude more than that.) Does anyone have any experience with the estimated TIV and what to expect as a normal range / how to know when something is wrong? Thanks so much! Best, Eli Diamond

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Problem with overlay of EPI analyze volume over T1 analyze volume in free surfer
by Salil Soman 21 Mar '06

21 Mar '06

Hi, I have been working with an image dataset of EPI images and MR images that have been registered in the freesurfer (transformation for which is stored in a .reg file). A T1 mgz volume was made using the following command: mri_convert -it analyze -ot mgh -i T1001.img -o T1.mgz I formed the EPI volume using the following command: mri_convert -it analyze -ot mgh -i F0001.img -o BH1.mgz when I load the T1 volume, and then overlay the EPI volume in tkmedit, with the reg file for transformation, I get a yellow box superimposed over a T1 image. The EPI volume itself appears to be properly formed, as I can read it directly into freesurfer and get a properly formed image. Was wondering if anyone had any suggestions as to what may be going wrong? Thanks, Salil Soman sal(a)bwh.harvard.edu

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autorecon2 failures
by Elizabeth Fenstermacher 21 Mar '06

21 Mar '06

Hey All, I have a few scans that I've been attempting to process that fail during autorecon2. I've eliminated all scan acquisitions that looked potentially problematic and attempted to rerun them. They both seem to go through autorecon1 without incident. The errors I'm getting are the somewhat ambiguous segmentation fault so I'm really not sure what manaul interventions should be attempted or might be useful to get them to run. Any suggestions would be greatly appreciated. Scans: /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991101rl-new/ /autofs/space/elvin_007/users/mci1/mci1_recon/batch2/991122so-new/ Thanks Eliz

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FSL/Freesurfer
by Clifford A. Smith, PhD 21 Mar '06

21 Mar '06

I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer? [Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] != 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff% ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Goldman, Aaron (NIH/NIMH) [C] 21 Mar '06

21 Mar '06

Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though. Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks, Aaron -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Aaron, Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)? thanks, Rahul On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote: > Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here. > > Thanks, > > -Aaron- > > -----Original Message----- > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Saturday, March 18, 2006 5:51 PM > To: Greg Harris > Cc: Freesurfer Mailing List; Karl Helmer > Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data > > Hi Greg, > > Could you send along jpegs or rgbs detailing what excactly the > parcellation atlas is doing in the cingulate region? Also have you looked > at both the white and pial surfaces in this area? > > Hope you are well othwerwise, > > Rahul > > On Sat, 18 Mar 2006, Greg Harris wrote: > >> Dear Karl, >> >> Has anybody had any success with the midline rois given by the atlas >> curvature.buckner40.filled.desikan_killiany that is automatically applied >> by autorecon3 under the newest stable release, version 3.0? >> >> Our trouble lies in the regions labeled corpuscallosum and >> <anything>cingulate: this >> atlas is giving us a corpus callosum that is exactly the ventral cingulate >> sulcus, and the 4 >> cingulate gyrus segments, which is what we are interested in in this case, >> incorrectly >> exclude their ventral portion. >> >> I presume this has been made to work at mgh, because Rahul Desikan's paper >> contains >> an illustration that is anatomically correctly labeled for these regions. >> >> We are providing an orig/001.mgz image to the autorecon1 step that is >> talairach aligned, >> skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed >> 16-bit >> T1-weighted MRI scan. We have thousands of them, collected over the past 15 >> years. >> We are writing a nifti .nii file, and converting it with >> >> mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 >> /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii >> /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz >> >> We actually mean to numerically measure the extent -- the area and thickness, >> say -- of >> anatomical regions of interest including <anything>cingulate and apply >> statistical tests to >> these data. A line of guff about Type I and Type II errors and what is only >> presumable >> when identifying anatomical rois would be of no interest, and considered >> needlessly >> defensive. After all, the other 29 regions of Desikan's really great atlas >> are in working >> order! >> >> Do we need to convince Rahul Desikan to release the "correct" >> *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 >> that correspond to his paper? >> >> Greg Harris >> The University of Iowa College of Medicine >> Psychiatry NeuroImaging Lab >> >> >> > > --

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RE: [Freesurfer] want to view one segmented subcortical object at a time...
by Goradia, Dhruman D 21 Mar '06

21 Mar '06

Hello Bruce and all, Is it possible to perform group analysis based only on a particular subcortical region of interest and visualize it? -Dhruman -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday 20 March 2006 16:20 To: Shahabuddin Ansari Cc: freesurfer(a)nmr.mgh.harvard.edu; Steve Pieper Subject: Re: [Freesurfer] want to view one segmented subcortical object ata time... Hi Shahab, we don't have anything to do that, although I think slicer probably can do it with our data. Bruce On Mon, 20 Mar 2006, Shahabuddin Ansari wrote: > Hello, > > I have segmented subcortical regions of the whole > brain from Freesurfer. Can somebody help me how to > view one object (say right hippocampus) at a time. > > Thanks > Shahab > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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