Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

pvr help
by Gautam, Prapti 13 Jun '13

13 Jun '13

Dear FreeSurfers I am trying to control for thickness in another surface using the pvr option in mri_glmfit. However, I'm confused as to how I can include the pvr option correctly in the contrast files. I have two groups, and would like to utilize DODS for this analyses as I think that my groups both have different intercepts and slopes. This is my fsgd set up : GroupDescriptorFile 1 Title MyTitle Class Controls CLASS FA Variables Age Input PMS1 Controls 14.442163 Input PMS2 Controls 14.354552 .. Input PMS7 FA 15.726215 Input PMS28 FA 14.45859 This is the command I run: mri_glmfit --y lh.surface.mgh --fsgd SA_age.fsgd --C con.mtx --surf fsaverage lh --cortex --glmdir test.glmdir --pvr lh.thickness.psc.mgh --pvr lh.thickness2.psc.mgh The contrast I would like to run is: 0 0 0 0 1 -1 so as to look at group interactions within thickness after controlling for another cortical surface. However, I can't get this to run as there is a "Matrix ill-conditioned" error. The contrast that does run is 0 0 0 0 1 (after passing only one pvr file). But this option seems to be neither dods nor doss. Is there a correct way to do a DODS analyses looking for interactions using the pvr option? Thank you, Prapti --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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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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