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30132 discussions

Extracting longitudinal rate stats using cluster annot files
by Robustelli, Briana (NIH/NIMH) [F] 30 Sep '11

30 Sep '11

Hello Freesurfer team, I have been running a longitudinal analysis and have just finished analyzing the data in qdec and running a cluster correction. I would now like to use the significant cluster annot files to extract the thickness rate stats for each subject and put them in a table. I am a little confused how to do this with a longitudinal dataset. It seems I am unable to use annotation2label with fsaverage to change the annot file to label files. What brain is qdec using to display the longitudinal results? Is it fsaverage as usual or a different average brain? From there I am not sure which directories to use to extract rate stats. Are they kept in the base directories or each time point (XX1, XX2, or XX1.long.XX_base)? I would really appreciate a step by step guide of which programs to use and on what files, to be able to extract stats for each subject using significant clusters as ROIs. I hope my question is clear and thank you for your time. Best, Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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Hippocampal Subfield Masks
by Shashwath Meda 30 Sep '11

30 Sep '11

Hi all - What would be the best way to create ROI masks of the individual hippo subfields that are generated in Freesurfer? Thanks! Shashwath Meda

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Re: [Freesurfer] Error due to fwhm
by Antonella Kis 30 Sep '11

30 Sep '11

Hi Doug, Thanks for helping me again. I used smoothing level of 20 because I was told to use this smoothing. If I use the 15 I am not getting the error but I need to use the 20.Is there a way that I can make it work/correct this error and get my tables cached in this case? Please advise. Thank you. AK ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>; "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu> Sent: Friday, September 30, 2011 10:52 AM Subject: Re: Error due to fwhm That exceeds the valued for which the tables are cached. What smoothing level did you use? doug Antonella Kis wrote: > > Hi, > > When I ran the QDEC on patients with abnormal side right, the fwhm for the clusters at thresh 2 is fwhm = 31.843147. > Then, I ran mri_glmfit-sim on the QDEC output and it gives me the following error (cannot find fwhm 32): > > ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd > > Is there a way that I can change the fhwm while running mri_glmfit-sim from 32 to 31.843147 or how I can correct this error? > > > Many thanks. > AK > > -- 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 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. Hi Doug,

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hippocampus segmentation
by George Kanw 30 Sep '11

30 Sep '11

Sorry to ask a trival question: After hippocampus segmentation, how can I extract the coordinates of each subregion? The general matlab functions seem unable to read the info. Thanks in advance, George

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Error due to fwhm (ASAP please)
by Antonella Kis 30 Sep '11

30 Sep '11

Hi Doug, I believe I got the error for the Abnormal Side R because the fwhm for the clusters with thresh 2 in QDEC is fwhm = 31.843147 as you can see below: and when I run mri_glmfit-sim it gives me the error: and when I run mri_glmfit-sim it gives me the error that cannot find fwhm 32: ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd Is three a way that I can change the fhwm while running mri_glmfit-sim from 32 to 31.843147 or how I can correct this error? MAny thanks. AK

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Tool for filling
by Ed Gronenschild 30 Sep '11

30 Sep '11

Hi, I'm looking for a tool to fill holes of only 1 voxel in size in a binary mask. I posted this also to the FSL mailing list but none of the suggested solutions could do this or were robust enough. Ed

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Concatenate surfaces
by MCLAREN, Donald 29 Sep '11

29 Sep '11

Is there a way to concatenate surfaces for use with mri_segstats? The surfaces are already in fsaverage space. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Error for Patients Abnormal Side Right
by Antonella Kis 29 Sep '11

29 Sep '11

Dear Doug, Seems that this will never end...It is so painful already. I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I was running: mri_glmfit-sim \ --glmdir lh_qdec_AbnormalSide_R.glmdir \ --cache 2 neg \ --cwpvalthresh .99 \ --overwrite and the ERROR: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/june2011/_orig_ FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/y.mgh --fsgd /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/qdec.fsgd dods --glmdir /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir --surf fsaverage lh --label /usr/local/freesurfer/subjects/june2011/_orig_/fsaverage/label/lh.aparc.label --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Diff-Class1-Class2-Intercept-thickness.mat DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 31.843147 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd PLEASE HELP! THANKS! AK

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aparc2feat and using Freesurfer Lookup Table
by Michelle Umali 29 Sep '11

29 Sep '11

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+ aseg.nii.gz -thr 433v uthr 433 \ featdir/reg/freesurfer/Visual_V3d_l.nii.gz The resulting image was empty. I was able to use aseg2feat for all subcortical regions, so then i used aparc2feat. However, this uses a different color table which is missing many of the regions present in the Freesurfer Color Lookup table that I would like to use. How can I get area 433 (Visual_V3d_l) from the Freesurfer Color Lookup Table so I can later run fslmaths to generate a mask? Thanks. Michelle

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Error with Clusters Summary (ASAP)
by Antonella Kis 29 Sep '11

29 Sep '11

Dear Doug, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after choosing the threshold 2. How can I correct this so --sim can cache my clusters from QDEC? If there is no way to correct this what should be my contrast vector if I want to eliminate AGE so I want to see the differences only between groups. In QDEC I did not choose age as covariant so I had only the discrete variable = Class. Should I take the contrast vector if I want to eliminate AGE to be equal with [1 -1] and my fsgd will not include the Age variable? MANY THANKS! AK

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