Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Fwd: Talairach Positioning in Horizontal View
by Peter Boulos 13 Jun '13

13 Jun '13

Hi Doug, I am using a GE 3T scanner with a slice thickness of 1.7 mm. I tried using the new script you provided (thanks for the help!) and it did not seem to make any difference with the couple of subjects that I tried. I have attached a screenshot. The right image in the screenshot is the original Talairaching and the left is after I ran the script you provided. Does this mean I will be forced into manually editing the Talairach for all of my subjects and re-running recon-all for all of them after I do that or is there another solution? Peter ----------------------------------------------------------------------------------------------------------- Message: 4 Date: Tue, 11 Jun 2013 13:41:47 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: Talairach Positioning in Horizontal View To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51B7615B.7000606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Peter, what scanner are you using? You might be better off with using a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that cleans it up. You can run just the talairaching with recon-all -s subject -schwartzya3t-atlas -talairach doug On 06/11/2013 01:03 PM, Peter Boulos wrote: > I am very new to the software and have just begun assessing Talairach > outputs for my subjects. I am confused in that I cannot seem to find a > balance I am happy with between positioning of the green lines in both > the horizontal and sagittal views for multiple subjects. I opened the > talairach output with the following command (tkregister2 --mgz --s > SUBJID --fstal --surf orig) and everything looked perfectly aligned > for all the subjects I have tried in both the coronal and sagittal > views but in the horizontal view the green lines went well off the > back of the brain. I have attached a screenshot. I tried to translate > the brain but that did not seem to solve my issue and I realized I > needed to scale the length of the brain. When I did that I was more > pleased with the outcome but the corpus callosum did not match up > nearly as well after I did that (second attached screenshot) and that > was the primary landmark I was using to pass my images in terms of > talairach output assessment. Do you have any advice for me? > > Peter > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Visualizing functional maps in tksurfer
by Reza Rajimehr 13 Jun '13

13 Jun '13

Hi, Using anatomical parcellation, I have labels for the occipital and temporal lobes in my subject. I have a functional map in the same subject that I want to show the activity only in the occipital and temporal cortex, and I want to mask the activity in the other parts of the cortical surface. How can I do this with FS-FAST/Freesurfer? Thanks, Reza ***************** Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University *****************

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Local GI - longitudinal analysis
by Pedro Rosa 13 Jun '13

13 Jun '13

Dear all, I have two issues: 1) I would like to run localGI in a longitudinal analysis. I runned the recon-all, the -base and the -long in all subjects. Then, I tried to run the -localGI command on .long. directories (I believe this it the directory I should run the command), the error below returned. How can I solve this issue? 2) I tried to download the 5.2 version, but the link does not seem to be working (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/) I tried both Chrome and Firefox. Regards, Pedro Rosa. ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.

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reg-feat2anat failure..
by Sudhin A. Shah 13 Jun '13

13 Jun '13

Hi, recon-all was successful. But when I try reg-feat2anat --feat '/home/..../func/2_reg' --subject xyz I get an error with MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): could not open file Loading mov Projecting LH Surfs Loading lh.white surf No such file or directory Thanks!

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Doubts on bblabel
by Anupa AV 13 Jun '13

13 Jun '13

Dear FS experts, By definition bblabel means.. Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the output. If a min is not specified, then -infinity is used. If a max is not specified, then +infinity is used. Example: bblabel --l lh.G_cuneus.label --o lh.out.label \ --xmin 0 --ymax -90 --zmin 10 --zmax 20 Keeps label points from lh.G_cuneus.label that have x > 0, y > -90, and z between 10 and 20. The result is stored in lh.out.label. IN THE ABOVE MENTIONED EXAMPLE, WHAT IS THE BASIS FOR THE SELECTION OF X, Y, Z VALUES??

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OptSeq2 eff and first order and contrast
by A a 13 Jun '13

13 Jun '13

Hello all, A question regarding the usage of Optseq2 I have this command line optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev ev40 2.5 20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o OptSeq_TRIALS/3_null9_6 --nsearch 10000 Now the efficiency tha I get is around 0.5. How I can tell this is a good or bad efficiency ? Is there a comparable level? Also if I would like to test for the first order effect of using a parametric modulation, can I test this using OptSeq2? Lastly, if I would like to test the efficiency of a contrast, say ev60 > ev20, how I do this ? Thanks Adnan

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Re: [Freesurfer] License problem
by Nick Jones 13 Jun '13

13 Jun '13

Regarding any license issue under Opensuse 12.3 and the libcrypt incompatibility. So grab a libcrypt from an older opensuse (one where freesurfer was working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then add the location to the LD_LIBRARY_PATH environment variable so that freesurfer finds the old libcrypt. There is another workaround but you must contact Nick Schmansky, I don't remember the details. Thanks Nick

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segmentation
by 小麦 13 Jun '13

13 Jun '13

Hi expert, How can I segment the white matter,gray matter and the cerebral hemisphere ,and rebuild the surface? Thanks in advance, Best wishes, lucy

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"ERROR:: Too many arguments." from recon-all / make_outer_surface
by Tudor Popescu 13 Jun '13

13 Jun '13

Hi all, The command: recon-all -s M19 -localGI resulted in: make_outer_surface('/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ERROR:: Too many arguments. I found a previous thread<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23414.html>in which someone was getting this error due to a space in the path, but my path doesn't have any spaces or any other dodgy characters. What could the problem be? Thanks. Tudor

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Editing masks
by Joshua deSouza 12 Jun '13

12 Jun '13

Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua

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Freesurfer June 2013