Freesurfer

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Troubleshooting: Are these pial and wm surface acceptable?
by xuemei lei 12 Jul '10

12 Jul '10

Hi All I recently started with FreeSurfer, and I am not sure about the pial and wm surface in the subcortical regions( eg. Hippocampus and amygdala,Medial temporal lobe). I have attatched the figures. Are these pial and wm surfaces acceptable? I have no ideas about the criterion and the right surface in this regions reconstracted by Freesurfer. Please let me know! thank you very much! -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 Email: bnuxuemei(a)gmail.com Blog: www.dubo.in Web: http://psychbrain.bnu.edu.cn ============================================== Welcome to the Blog: www.dubo.in

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HELP
by Asaf Kaftory 12 Jul '10

12 Jul '10

unsubscribe me thanks. ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Mon, July 12, 2010 8:09:19 AM Subject: Freesurfer Digest, Vol 77, Issue 22 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Displaying significant difference with a threshold of cluster size (Douglas N Greve) 2. Re: Displaying significant difference with a threshold of cluster size (liang wang) 3. Troubleshooting: Are these pial and wm surface acceptable? (xuemei lei) ---------------------------------------------------------------------- Message: 1 Date: Sun, 11 Jul 2010 13:42:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Displaying significant difference with a threshold of cluster size To: liang wang <wanglbit(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4C3A028F.7070800(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You should correct for multiple comparisons using cluster-wise correction. See the tutorials on group analysis on our wiki. doug liang wang wrote: > Hi, > > Using mri_glmfit, I found significant between-group difference in > cortical thickness in some regions. However, there are a lot regions > with very small vertices surviving the given threshold. What I need to > do is displaying large clusters (e.g. having 20 vertices at least) > assumed as "true" difference. I don't know how to make it by a > selected threshold of cluster size . Any suggestions would be appreciated. > > Liang > > -- > Liang Wang, PhD > Postdoctoral Fellow > Woodward Lab > Department of Psychiatry > University of British Columbia > BC Mental Health & Addiction Services > 938 West 28th Avenue > Vancouver BC V5Z 4H4 > Telephone: 1-604-875-2000 (ext. 4735) > Fax: 1-604-875-3871 > Email: wanglbit(a)gmail.com <mailto:wanglbit@gmail.com> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 ------------------------------ Message: 2 Date: Sun, 11 Jul 2010 11:16:17 -0700 From: liang wang <wanglbit(a)gmail.com> Subject: Re: [Freesurfer] Displaying significant difference with a threshold of cluster size To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTinU0knZdFiivSrtnnF4LuV_SlK5iH7eftriOV1-(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello Doug, Thanks for your kind response. I have tried to use mri_glmfit-sim to correct the results. However, no significant differences were observed. To compare with other studies, I would like to report the results (p < 0.001, uncorrected) and mention that they will disappear if corrected by cluster-based threshold method. Is it a acceptable way? Liang 2010/7/11 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > You should correct for multiple comparisons using cluster-wise correction. > See the tutorials on group analysis on our wiki. > > doug > > liang wang wrote: > >> Hi, >> >> Using mri_glmfit, I found significant between-group difference in cortical >> thickness in some regions. However, there are a lot regions with very small >> vertices surviving the given threshold. What I need to do is displaying >> large clusters (e.g. having 20 vertices at least) assumed as "true" >> difference. I don't know how to make it by a selected threshold of cluster >> size . Any suggestions would be appreciated. >> >> Liang >> >> -- >> Liang Wang, PhD >> Postdoctoral Fellow >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: wanglbit(a)gmail.com <mailto:wanglbit@gmail.com> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > 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 > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Troubleshooting: Are these pial and wm surface acceptable?
by xuemei lei 11 Jul '10

11 Jul '10

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FDR correction in Qdec
by Xiaojing Long 10 Jul '10

10 Jul '10

Hi, all, I have some questions about performing the FDR correction in Qdec. I ran recon-all on all my subjects, then ran the surface group analysis following the Qdec tutorial. There are 3 factors in the qdec.table.dat file: age, gender and diagnosis. In the Design tab of Qdec, I selected the discrete factor 'diagnosis' for analysis. When the analysis was done, there is a description "Does the average thickness differ between Diseased and Normal?" in the Display tab. I think this should be the uncorrected map. Then I tried to run the FDR correction for multiple comparisons. I set the rate to be 0.05 and 0.01 respectively. However, I found no difference between the results using different rates. In the Terminal, the information are also the same: "MRISfdr2vwth(): np = 163842, nv = 163842 Found 107008 of 163842 vertices above FDR threshold (of 1.48619)" I wonder whether I did the analysis correctly. Are such results possible or reasonable? Thank you in advance. Best, Xiaojing

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left right reversal
by YUMI MAEDA 09 Jul '10

09 Jul '10

Hi, I am trying to do left right reversal of surface by following this link, http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(rever… after recon-all -subcortseg -s LRflipped-subject", I tried to check the result with tksurfer with 'tksurfer LRflipped-subject hemi inflated'. Then I got this error message that MRISread(/freesurfer//LRflipped-subject/surf/lh.inflated): could not open file No such file or directory tksurfer.bin: could not read surface file /freesurfer//LRflipped-subject/surf/lh.inflated. No such file or directory Here is my question, Is this /surf/lh.inflated files supposed to be produced when I follow the step described in the link? Or Is there any more step which is not written on the link? YUMI

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Left Right reversal
by Yumi Maeda 09 Jul '10

09 Jul '10

Hi, I am trying to do left right reversal of surface with the instruction of this link below. http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(rever… After recon-all -subcortseg -s LRflipped-subject, I tried to see the result with this command , 'tksurfer LRflipped-subject hemi inflated'. There is this error message, MRISread(/////freesurfer//LRflipped-subject/surf/lh.inflated): could not open file No such file or directory tksurfer.bin: could not read surface file /////freesurfer//LRflipped-subject/surf/lh.inflated. No such file or directory How can I get surf/lh.inflated ? Is there any step that was not written on this instruction? YUMI

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data analysis/reduction after autorecon3
by Liukarl 09 Jul '10

09 Jul '10

Hello, Freesurfers After autorecon3, there are cortical measures for the over 30 predefined regions. And for each regions, there are area, volume, and thickness 3 different measures, which means there are approximately 200 measure for both hemispheres. As a preliminary analysis without specific priori hypothesis, what is the standard way to examine the massive data to find possible group difference for a small sample size about 40 subjects with 20 in each group. thanks Karl _________________________________________________________________ 想知道明天天气如何？必应告诉你！ http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ2

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"Configure Overlay Display" tksurfer window...
by Gonzalo Rojas Costa 09 Jul '10

09 Jul '10

Hi: How can I display an overlay in such a manner that only values between "min" and "max" are displayed in a color palette, and values less than "min" and values greater than "max" are displayed in gray ?... Sincerely, Gonzalo Rojas Costa

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recon-all not finishing properly
by p.s.bjerkan＠studmed.uio.no 08 Jul '10

08 Jul '10

Hi, Have a question regarding one subject I´m trying to run with recon-all. It´s been run successfully before. The Freesurfer version used is 4.0.4. We discovered one subject having faults, and when checking recon-all-status.log, it is clear that -autorecon2 does not finish properly. The last entry is "ASeg Stats". The step "Cortical ribbon mask" is thus not included. The "recon-all finished with ERRORS" is not listed. The last entry after -autorecon3 is "AParc-to-ASeg", "WMParc" is not finished. The recon-all-status.log file is about 4.1 GB! Therefore difficult to scan the text, but an excerpt of something repeated is: -------------------------------------------------------------------------- No such file or directory MRIScomputeWhiteVolume: src (11, 257, 296) maps to (345, 137, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 297) maps to (345, 137, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 298) maps to (345, 138, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 299) maps to (345, 138, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 300) maps to (345, 138, 147) - OOB No such file or directory -------------------------------------------------------------------------- Have tried to run it several times. Thankful for any suggestions on what to do! Thanks! Petr

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cortical thickness more than 5 milimeters...
by Gonzalo Rojas 08 Jul '10

08 Jul '10

Hi: Sometime ago I asked about how to show cortical thickness more than 5 milimeters... Bruce answered me, but I could not find his answer... Could you please send me again ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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