[Freesurfer] A few questions regarding Monte Carlo and mri_glmfit
Hello Freesurfer Gurus, I have been conducting cortical thickness and LGI analyses at my lab using Qdec. We have gotten some really promising results thanks to your help! However I have a few withstanding questions which need answered to make sure our results are methodologically valid: 1) After we would display our results in Qdec, I would then run Multiple Comparison tests on the data (the FDR and Monte Carlo Simulation). However, when we would run the Monte Carlo we would get a larger surface area of significance than was shown with the original display at a threshold of +/- 2. Is this the same function that is run with mri_glmfit--sim as seen here ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons )? I understand that the area of significance may be larger post MC because the iterations allow the MAXIMUM size cluster to be shown. Is this correct? If so, how do I correctly interpret these results? Am I right in assuming that as long as the original significance area we see is still reported by the Monte Carlo to be significant then our findings are statistically significant? 2) My second question is in regard to Qdec`s inability to have discrete factors which contain more than two levels. I was trying to use handedness as a discrete factor, but since our rating has three levels (left handed, ambi, and right handed), the analysis obviously wouldn`t work. Instead, I deleted the .levels files in the qdec file and saw that Qdec then accepted handedness as a continuous variable. When I ran the analyses using Qdec as a `pseudo-continuous` variable it worked! I know I got a little creative and could have done this actually using handedness with three levels with mri_glmfit it`s just that I had very limited time to do this and wanted to see if this way worked. Is this somehow invalid? I don`t know enough about the functions Qdec runs to know. Thank you so much for your time and help! All the best, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Can one adjust CWP Threshold in Qdec?
Hi Freesurfer Experts, I was wondering if there is a way for me to adjust the default CWP of p .01 to p .05 on Qdec? I saw that it is possible using cwpvalthresh .05 with glmfit, but as I have set up everything with Qdec, it would be much easier and save me time to do this via Qdec. Thanks so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Issue with smoothing in local gyrification process
Hello Freesurfer Gurus, I am trying to compute LGI analysis using Qdec and have successfully loaded my qdec.table.dat file as well as created .Qrecrc to include the new pial_lgi measure. However, when I try to analyze using this measure (or with any measure for that matter), an error pops up saying that it was not able to locate the fwhm10.fsaverage.mgh file. I am guessing that this is the smoothed file and therefore that I need to run recon-all -qcache -measure pial_lgi -average -s, but when I run this while in my subjects directory, it tells me the -average flag is unrecognized. (I also tried this with -fsaverage and got the same error). Can you please help troubleshoot what might be going on? The lh pial files have already been created. When those are created I am guessing the smoothed files aren't created automatically as well? I was getting these instructions from the Schaer article here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/#!po=31.2500 Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Error with asegstats2table function
Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' [dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt Password: ERROR: SUBJECTS_DIR environment variable not defined! Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt ERROR: output table name should be specified (use --tablefile FILE) Please help! I have tried everything I can think of. Thank you for everything, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Error when completing cortical thickness analysis
I am conducting cortical thickness analyses between hundreds of individuals for a study we are conducting. I was getting this error Unrecognized sub-option flag 'annot_outline'. and so I tried to do the group analysis tutorial and input the command from the end of it (please see command below) but still got the same error. Freeview would open but it would not show any images. Could you help me to resolve this issue please? Also, what does it mean when it spits out invalid drawable? freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Error when launching qdec
Hello Freesurfer Community, I am now having issues getting qdec to launch as well. The qdec window pops up momentarily but then disappears. This is the error message I get: error: xp_attach_gl_context returned: 2 X Error of failed request: 0 Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 26 (X_GLXMakeContextCurrent) Serial number of failed request: 1157 Current serial number in output stream: 1157 Could XQuartz somehow be the problem? I am now running XQuartz 2.7.5 on my Mac that`s in Mavericks. Thank you so much again for all of your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Bus error still when trying to launch tksurfer
Hello again Bruce, Thanks so much for your reply. I tried uninstalling XQuartz completely and reinstalling it, and I`m still getting the bus error. I have XQuartz`s newest version (2.7.7) that was launched in August of this year installed and it works with Macs 10.6 and newer. My Mac environment is such: Mac OS X Snow Leopard 10.6.8 Memory: 4GB 1067 MHz DDR3 Model Name:iMac Model Identifier:iMac10,1 Processor Name:Intel Core 2 Duo Processor Speed:3.06 GHz Number Of Processors:1 Total Number Of Cores:2 L2 Cache:3 MB Memory:4 GB Bus Speed:1.07 GHz Boot ROM Version:IM101.00CC.B00 Any further ideas what might be going on? Do I need a newer version of OS X in order to use Freesurfer optimally? Thank you so much again for your time! All the best, Claire On Mon, Oct 20, 2014 at 6:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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. GLM contrast vector for continuous variable interaction (Bronwyn Overs) 2. Bus error when trying to launch tksurfer (Claire Morley) 3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi) 4. Re: Bus error when trying to launch tksurfer (Bruce Fischl) 5. Do not have 'recon edit' button! Please help! (Smaragdi A.) 6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl) 7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.) 8. unpacksdcmdir (Alshikho, Mohamad J.) 9. Re: unpacksdcmdir (Shantanu Ghosh) 10. Re: unpacksdcmdir (Douglas N Greve) 11. Re: GLM contrast vector for continuous variable interaction (Douglas N Greve) -- Message: 1 Date: Mon, 20 Oct 2014 09:33:13 +1100 From: Bronwyn Overs b.ov...@neura.edu.au Subject: [Freesurfer] GLM contrast vector for continuous variable interaction To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 54443c29.9000...@neura.edu.au Content-Type: text/plain; charset=iso-8859-1 Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.5 0.50.50.5 000000000.50.50.50.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0001.html -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 13292 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0004.png -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1233 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0005.png -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 834 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0006.png -- next part
[Freesurfer] Bus error when trying to launch tksurfer
Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script: DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemiis rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal). Thanks so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot* ___ Freesurfer mailing list Freesurfer@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.
