Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Hippocampal subfields intensity
by Marcos Martins da Silva 10 Jun '13

10 Jun '13

Hi, Freesurfer Experts After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.5748 46.0000 105.0000 59.0000 How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step. Thank you in advance for any help. Marcos

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OptSeq first time
by fMRI 10 Jun '13

10 Jun '13

Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. My design will have two columns : main effect of moving hand and the 1 order. My contrast will be like this [1 0; 0 1] This is what I would like to optimize using OptSeq2: Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds I am not sure whether I should use null events or the Period between movement is enough. Also my main aim is to optimize the best design in terms of detection. Please any guide or help Thanks AS

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Re: [Freesurfer] white matter volume per lobe...
by Gonzalo Rojas Costa 10 Jun '13

10 Jun '13

Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa > Message: 15 > Date: Mon, 27 May 2013 22:41:41 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] white matter volume per lobe... > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51A41965.6050808(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > you will need to run mri_annotation2label and specify the output to be > an annotation file instead of a segmentation. Then you will have to run > mri_aparc2aseg, specifying your lobes annotation as well as --labelwm > (look in the recon-all.log file for an example of how wmparc.mgz is > created). Then run mri_segstats (you can also get an example from the > recon-all.log file). > doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Surface area measurement method
by Andreas Berger 10 Jun '13

10 Jun '13

Hello FreeSurfers, after reading this [1] paper about measuring surface area, i realized i don't know what the default way of measuring surface area is in FreeSurfer. Is it similar to what's described in the paper? Could you point me to the right documentation or publication? Forgive me if i've overlooked it, i found something for thickness, but not for area. To clarify, i don't mean parcellation-based areas, i mean the measure that i find in /surf/hemi.area. thanks, regards, Andreas [1] Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43

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surface stream steps
by Joshua Lee 10 Jun '13

10 Jun '13

Dear Freesurfers, >From the Wiki Freesurfer surface stream follows something like: 1. Affine registration to Tal. 2. Bias correction and skull stripping 3. Classify WM 4. Cut hemisphere planes 5. Tile WM surface 6. Refine WM surface following GM-WM intensity gradients 7. Nudge (nudge?) WM surface to follow the GM-CSF gradient to generate pial surface 8. Labeling Data Set 9. Stats May I ask which couple of these steps tend to be the most computationally taxing/longest to complete? Also, I'm not sure I understand #7. Is the WM surface scaled in some sense to approximate the GM-CSF boundary, or is this just a refinement step like #6 of a surface that already approximates the GM-CSF boundary? Thanks, I've spent most of my time working with the sub-cortical stream. - Joshua

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volume called 001.mgz
by Varghese Chikku 10 Jun '13

10 Jun '13

Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni freesurfer@freesurfer-VirtualBox:~$ recon-all -i /home/freesurfer/Desktop/10035BL/T1pre/Image00001 -autorecon-all -s 10035BLFS Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/10035BLFS mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image00001 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image00001 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz file not found or unknown file type for file /home/freesurfer/Desktop/10035BL/T1pre/Image00001 #-------------------------------------------- #@# MotionCor Mon Jun 10 16:03:45 CEST 2013 ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/10035BLFS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013 For more details, see the log file /usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting freesurfer@freesurfer-VirtualBox:~$

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Installation trouble on Macbook Air (no such file or directory)
by nmw 10 Jun '13

10 Jun '13

I am new to Unix and FreeSurfer, and I am having some trouble installing FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just fine, and when I start the installation steps, I'm instructed to add some lines to my .cshrc or .tcshrc files in my home directory. Can anyone point me to this file? Also, just below on the installation dialog, it says for sh or bash users: export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Can I use these instead of the first two lines of code? I tried to enter these bash lines one at a time into my terminal window. The first one ("export") did not give me any errors but for the "source" one, I received the message: bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory. Any idea as to why I am getting this error? My apologies in advance for my lack of experience. Many thanks, Nate

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Coupling cortical and TRACULA results
by stdp82＠virgilio.it 10 Jun '13

10 Jun '13

Hi list, Thiebaut de Schotten et al., in an article on cortex ("Monkey to human comparative anatomy of the frontal lobe association tracts" reported that "The superior longitudinal fasciculus has three distinct branches (Petrides and Pandya, 1984). In humans, the first branch of the superior longitudinal fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third branch (SLF III) connects the intraparietal sulcus and inferior parietal lobule to the inferior frontal gyrus (BA 44, 45, 47)" By TRACULA output we have 2 output SLFp and SLFt. Having also cortical results, I wonder if possible to know which are the seed and target areas of SLF p and SLFt or al least to know which is that branch that is described by SLFp output. Thanks, Stefano

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Re: [Freesurfer] CVS and group analysis
by Lilla Zollei 09 Jun '13

09 Jun '13

Do you want to compute the average intensity volume after the CVS registration steps? YOu could use mri_average with the "final_CVSmorphed_tocvs_avg35.norm.gz" files as input images. Lilla On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: > Sorry. I'm talking about "final_CVSmorphed_tocvs_avg35.norm.gz"Thanks for the very prompt reply > F > > 2013/6/9 Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > Hi, Can you be more specific? What files / volumes do you want to compute a group average of? > > On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: > > Hi freesurfers, After doing cvs registration, how can I make a group average? Is fsaverage OK? > Thanks > > > > _______________________________________________ > 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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CVS and group analysis
by Fernando Valle-Inclán 09 Jun '13

09 Jun '13

Hi freesurfers, After doing cvs registration, how can I make a group average? Is fsaverage OK? Thanks

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Freesurfer June 2013