[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] Visual Check
Hi everyone, After pre-process recon-all，what parts of its process need to check visually ?how to determine its necessity for check ? and how to check them ? Could you provide me for a guide or pipeline? Best regards. Xin-Fa Shi. ___ 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] Registration
After 'recon-all' ,how to check its accuracy of registration ? what anatomy should be paid more attention ? Best regards . Xin-Fa Shi . ___ 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.
Re: [Freesurfer] Registration
Hi Xin-Fa the easiest way to check the quality of the cortical registration is to look at one of the parcellations (e.g. lh.aparc.annot) and see if it labeled the major sulci correctly cheers Bruce On Fri, 12 Dec 2014, Xinfa Shi wrote: After 'recon-all' ,how to check its accuracy of registration ? what anatomy should be paid more attention ?Best regards . Xin-Fa Shi . ___ 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.
Re: [Freesurfer] Visual Check
Hi Xin-Fa scroll through your data with the surfaces overlaid on the volume and make sure that they follow where you think the gray/white and pial boundaries are and do the same for the aseg.mgz cheers Bruce On Fri, 12 Dec 2014, Xinfa Shi wrote: Hi everyone, After pre-process recon-all，what parts of its process need to check visually ?how to determine its necessity for check ? and how to check them ? Could you provide me for a guide or pipeline? Best regards. Xin-Fa Shi. ___ 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] freesurfer gpu acceleration using amd video cards?
Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video cards? Thanks, Salil Soman, MD, MS ___ 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] functional data on freeview
Dear freesurfer users, I have installed freesurfer and freeview. The visualization of brain surfaces looks great. Is it possible to visualize functional MEG/EEG source data with freeview? What I have: 1. Source locations (Nx3) 2. Activation strength (Nx1) at these locations 3. The anatomy data from the same subject, processed by freesurfer. 4. Softwares, matlab2014b, freesurfer v5.3, MNE2.7.4 Thank you very much! best Peng ___ 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.
Re: [Freesurfer] functional data on freeview
Hi Peng yes, for sure. This is what Matti Hamalainen's excellent MNE package is designed for. I'll cc Matti so he can chime in cheers Bruce On Fri, 12 Dec 2014, peng wrote: Dear freesurfer users, I have installed freesurfer and freeview. The visualization of brain surfaces looks great. Is it possible to visualize functional MEG/EEG source data with freeview? What I have: 1. Source locations (Nx3) 2. Activation strength (Nx1) at these locations 3. The anatomy data from the same subject, processed by freesurfer. 4. Softwares, matlab2014b, freesurfer v5.3, MNE2.7.4 Thank you very much! best Peng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] freesurfer gpu acceleration using amd video cards?
Its my understanding is that CUDA is specific only to NVIDIA graphics devices. http://www.nvidia.com/object/cuda_home_new.html -Zeke On 12/12/2014 08:54 AM, Salil Soman wrote: Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video cards? Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Apply a label to longitudinal measures and extract stats
Dear experts, I have created a label from Qdec and used mri_label2label to apply it to all subjects. Now I need to extract the pc1 measure from longitudinal analysis in my label. Would you please advise how to do this since kris_anatomical_stats doesn't work here? Best regards, Amirhossein Manzouri ___ 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.
Re: [Freesurfer] trac-all -path error Segmentation Fault (Core Dumped)
Ack. Can't believe I missed that. Thank you. I'll run it again and see how that turns out. On Thu, Dec 11, 2014 at 2:07 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Thomas - No bother at all! If you search for the word error in your trac-all.log, you'll see that it couldn't find the MNI template, which means that some of the pre-processing steps did not complete. You can either remove the mnitemp line from your configuration file (so that it uses the default $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) or edit that line to include the correct path to the MNI template. You'll then need to rerun the pre-processing, or at least the steps including the inter-subject registration and beyond (run trac-all without arguments to see the sequence of steps included in the pre-processing). Hope this helps, a.y On Wed, 10 Dec 2014, Thomas DeRamus wrote: Freesurfer Experts, Sorry to bother you again, but I'm having an issue with the 3rd step of Tracula. I was able to run -prep just fine, and I ran bedpostx locally (there was an error in the step 2 command apparently, used command bedpostx /path/subj/dmri/), but every time I run the third step with the -path command I get the error Segmentation fault (core dumped) foreach: No match. The foreach error has me thinking there is something wrong with my dmrirc file or my folder structure. I'd appreciate any feedback you are willing to give on this error. I've attached the trac-all.log for one subject, but it gives the same error even when different subjects are used or this one is removed. -- Thomas DeRamusUAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 Phone: 205-934-0971 Email: tpdera...@gmail.com, faus...@uab.edu ___ 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. -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu ___ 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.
Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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.
Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
The file I looked at had a bunch of carriage returns (try looking at it with more or less or cat). As long as those are in there, it will create an error. Try running this and using the new one cat g4v1.73.fsgd | sed 's/\r/\n/g' new.g4v1.73.fsgd On 12/12/2014 12:09 PM, lindsay hanford wrote: Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com wrote: Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com wrote: Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study| *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 tel:905%20525%209140%20x24784***|*lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study| *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784***|*lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] Command '-qa' in TRACULA
Are you sure your path isn't look for the older trac-all first? If you didn't remove/overwrite it, that is. Type which trac-all (without the quotes) and see if the correct one is shown. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anri WATANABE [z2aa...@koto.kpu-m.ac.jp] Sent: Friday, December 12, 2014 1:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] Command '-qa' in TRACULA I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all -corr -c the_name_of_my_configuration_file, but it failed. I pasted the log below and do you have any advices? Thank you, Anri [watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- -I omitted a part of log in an image correction step- Computing mean across frames Writing to /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz bet /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain_mask.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_002/dlabel/diff #- trac-preproc finished without error at Fri Dec 12 14:04:04 JST 2014 [watanabeanris-Mac-Pro:~] watanabeanri% trac-all -qa -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial ERROR: flag -qa unrecognized -qa -c /volumes/mybook/Anri/diffusion_tutorial/dmrirc.tutorial [watanabeanris-Mac-Pro:~] watanabeanri% ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 11:38 GMT+09:00 Anri WATANABE z2aa...@koto.kpu-m.ac.jpmailto:z2aa...@koto.kpu-m.ac.jp: Thanks, Anastasia. I'm worried about that a quality assessment step is not run because there are no presentation about -qa when I type trac-all in terminal (other steps are presented.) Do you mean QA step will be run even if no mention about it? Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu: Hi Anri - This is not a command itself, it's an option of the trac-all command. So you need to run: trac-all -qa -c the_name_of_your_configuration_file Or, if you just run the entire preprocessing: trac-all -prep -c the_name_of_your_configuration_file then the motion QA measures will be computed by default as one of the many steps of the preprocessing. You can run trac-all without any arguments to see usage information on all the the different options. Hope this helps, a.y On Tue, 9 Dec 2014, Anri WATANABE wrote: Thank you, Anastasia. I had downloaded the updated software and unzipped it, but I couldn't find the command -qa. I found -qa in the trac-all text file in the updated software. However there are no -qa in terminal when I run trac-all. Do I have to move the file somewhere? ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu: Hi Anri - See here, and follow the link software update: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The -qa option was added after 5.3 was released. a.y On Mon, 10 Nov 2014, Anri WATANABE wrote: Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and
Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)
I'm pretty sure this is due to the language locale settings. Can you do an experiment? Run echo $LANG if the result is not en_US.utf8 try setenv LANG en_US.utf8 And see if that fixes it. If it does, I can change the script doug On 12/11/2014 03:11 AM, Milde, Christopher wrote: Dear Doug, Unfortunately, it doesn't make a difference if I'm using a dot or comma or simply type in 2 or 3 as a threshold. The terminal output always shows me the converted version with a comma 2.3 -- 2,3 or 2 -- 2,0 which is not recognized by the command. Maybe I have to change the default settings of floats in the bash using printf? Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Mittwoch, 10. Dezember 2014 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: Dear Doug, I tried to run MCC with cluster-sess but unfortunately I got the same error message like when I'm using mri_glmfit-sim. It does not recognize the thresh (cluster-forming thresh) Here is the terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/christopher/Desktop/freesurfer FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects MNI_DIR /home/christopher/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1 [christopher@fu20a S1]$ cd $proj_dir [christopher@fu20a S1]$ [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Montag, 24. November 2014 20:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Getting voxel values from aseg.mgz
You can also use mri_binarize which has more documentation :-) On 12/11/2014 01:31 AM, pradeep mahato wrote: There is no documentation or example for mri_extract_label. What should be the syntax for it. What kernel and xform file should be used. On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you can use mri_extract_label to copy just the hippocampal labels out of the segmentation if that is what you mean. The values for left and right hippocampus (17 and 53) can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Wed, 10 Dec 2014, pradeep mahato wrote: After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using mri_convert with multiframe dicom
Sorry, I never got around to downloading them and now they are gone. Can you re-upload them? doug On 12/08/2014 06:07 PM, Gurney, Jenny wrote: Hi all, Doug, just wondering if anyone has had time to look into the issue of using mri_convert with multiframe/enhanced DICOM. My colleague, Lauren Wallace drop boxed (via your dropbox) some sample phantom data in this format back in October, I believe. (I also work with John Flavin who raised the issue on the board in October.) We’re seeing this data format coming from several institutions. Seems like others must be running into this. Thanks! Jenny Gurney CNDA/Wash U The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Thank you Doug! I replaced all my spaces with new spaces and it worked! Much appreciated! Lindsay On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] funcroi-table-sess error, \set: Variable name must begin with a letter\
Hi there, I'm having the same problem referenced in this thread from last year. When I send the command: funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 I get the following error: set: Variable name must begin with a letter. I was wondering if there was any resolution to this issue when it came up last year or if you have any advice on how I should proceed now. I do have a folder named log in the directory I'm running the command from. Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Interdisciplinary Affective Science Lab Massachusetts General Hospital Department of Psychiatric Neuroscience (p) 617.643.6347 (f) 617.726.5760 k...@nmr.mgh.harvard.edu ___ 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.
Re: [Freesurfer] Command '-qa' in TRACULA
Does a file called dmri/dwi_motion.txt get created? That's the output of the QA step. This is explained in the tutorial, under Outputs from quality assessment: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs On Fri, 12 Dec 2014, Anri WATANABE wrote: Thanks, Anastasia.I'm worried about that a quality assessment step is not run because there are no presentation about -qa when I type trac-all in terminal (other steps are presented.) Do you mean QA step will be run even if no mention about it? Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Anri - This is not a command itself, it's an option of the trac-all command. So you need to run: trac-all -qa -c the_name_of_your_configuration_file Or, if you just run the entire preprocessing: trac-all -prep -c the_name_of_your_configuration_file then the motion QA measures will be computed by default as one of the many steps of the preprocessing. You can run trac-all without any arguments to see usage information on all the the different options. Hope this helps, a.y On Tue, 9 Dec 2014, Anri WATANABE wrote: Thank you, Anastasia. I had downloaded the updated software and unzipped it, but I couldn't find the command -qa. I found -qa in the trac-all text file in the updated software. However there are no -qa in terminal when I run trac-all. Do I have to move the file somewhere? ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Anri - See here, and follow the link software update: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The -qa option was added after 5.3 was released. a.y On Mon, 10 Nov 2014, Anri WATANABE wrote: Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and could neither find the context about quality assessment step nor run the command 'trac-all -qa -c configulation file. I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion (64-bit). Could anyone solve this problem? Thank you. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ 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 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
Re: [Freesurfer] Command '-qa' in TRACULA
If the -qa flag is not recognized, then you're still running the old version of trac-all, not the updated version. On Fri, 12 Dec 2014, Anri WATANABE wrote: I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all -corr -c the_name_of_my_configuration_file, but it failed.I pasted the log below and do you have any advices? Thank you, Anri [watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- -I omitted a part of log in an image correction step- Computing mean across frames Writing to /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz bet /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain_mask.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_002/dlabel/diff #- trac-preproc finished without error at Fri Dec 12 14:04:04 JST 2014 [watanabeanris-Mac-Pro:~] watanabeanri% trac-all -qa -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial ERROR: flag -qa unrecognized -qa -c /volumes/mybook/Anri/diffusion_tutorial/dmrirc.tutorial [watanabeanris-Mac-Pro:~] watanabeanri% ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 11:38 GMT+09:00 Anri WATANABE z2aa...@koto.kpu-m.ac.jp: Thanks, Anastasia.I'm worried about that a quality assessment step is not run because there are no presentation about -qa when I type trac-all in terminal (other steps are presented.) Do you mean QA step will be run even if no mention about it? Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Anri - This is not a command itself, it's an option of the trac-all command. So you need to run: trac-all -qa -c the_name_of_your_configuration_file Or, if you just run the entire preprocessing: trac-all -prep -c the_name_of_your_configuration_file then the motion QA measures will be computed by default as one of the many steps of the preprocessing. You can run trac-all without any arguments to see usage information on all the the different options. Hope this helps, a.y On Tue, 9 Dec 2014, Anri WATANABE wrote: Thank you, Anastasia. I had downloaded the updated software and unzipped it, but I couldn't find the command -qa. I found -qa in the trac-all text file in the updated software. However there are no -qa in terminal when I run trac-all. Do I have to move the file somewhere? ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Anri - See here, and follow the link software update: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The -qa option was added after 5.3 was released. a.y On Mon, 10 Nov 2014, Anri WATANABE wrote: Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and could neither find the context about
[Freesurfer] Freesurfer version compatibility
Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points. The question is we currently have version 5.3 running on our server. Is it okay to add the control points and run the segmentation again with version 5.3? (recon-all --subjid sub1 autorecon2-cp autorecon3) Is there other suggestions? Thank you in advance Deniz ___ 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.
Re: [Freesurfer] Freesurfer version compatibility
Hi Deniz if you rerun them all with 5.3 that should be ok Bruce On Fri, 12 Dec 2014, Deniz Ozgen wrote: Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points. The question is we currently have version 5.3 running on our server. Is it okay to add the control points and run the segmentation again with version 5.3? (recon-all --subjid sub1 autorecon2-cp autorecon3) Is there other suggestions? Thank you in advance Deniz ___ 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.
Re: [Freesurfer] Command '-qa' in TRACULA
No, she is saying that you should open a terminal, and type only trac-all. This should display the help for that program, including the program's flags. If you don't see -qa listed, then the trac-all you're using is an older version. You need to verify that you have downloaded the latest version and overwritten the older one (or change your $PATH to look for the newer one). On 12/11/2014 09:38 PM, Anri WATANABE wrote: Thanks, Anastasia. I'm worried about that a quality assessment step is not run because there are no presentation about -qa when I type trac-all in terminal (other steps are presented.) Do you mean QA step will be run even if no mention about it? Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu: Hi Anri - This is not a command itself, it's an option of the trac-all command. So you need to run: trac-all -qa -c the_name_of_your_configuration_file Or, if you just run the entire preprocessing: trac-all -prep -c the_name_of_your_configuration_file then the motion QA measures will be computed by default as one of the many steps of the preprocessing. You can run trac-all without any arguments to see usage information on all the the different options. Hope this helps, a.y On Tue, 9 Dec 2014, Anri WATANABE wrote: Thank you, Anastasia. I had downloaded the updated software and unzipped it, but I couldn't find the command -qa. I found -qa in the trac-all text file in the updated software. However there are no -qa in terminal when I run trac-all. Do I have to move the file somewhere? ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu: Hi Anri - See here, and follow the link software update: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The -qa option was added after 5.3 was released. a.y On Mon, 10 Nov 2014, Anri WATANABE wrote: Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and could neither find the context about quality assessment step nor run the command 'trac-all -qa -c configulation file. I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion (64-bit). Could anyone solve this problem? Thank you. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] funcroi-table-sess error, \set: Variable name must begin with a letter\
I can't remember what the issue was. Can you run funcroi-table-sess -debug -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 | tee dng.log and send me dng.log doug On 12/12/2014 03:03 PM, Morenikeji Adebayo wrote: Hi there, I'm having the same problem referenced in this thread from last year. When I send the command: funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 I get the following error: set: Variable name must begin with a letter. I was wondering if there was any resolution to this issue when it came up last year or if you have any advice on how I should proceed now. I do have a folder named log in the directory I'm running the command from. Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Interdisciplinary Affective Science Lab Massachusetts General Hospital Department of Psychiatric Neuroscience (p) 617.643.6347 (f) 617.726.5760 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] surface check
Hi everyone , After recon-all，how to determine quickly the quality of whiter matter segmentation ,surfaces(e.g. whiter matter surface and pial surface) and topological fix ? what anatomy should be paid more attention? Best regards? Xin-Fa Shi . ___ 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.
