[Freesurfer] low polygon count like fsaverage3
Hello again, I am still looking for a way to create a low polygon surface during recon-all (where labels still fit). Is there any (expert) option where I can specify the number of vertices or distance between vertices? How was fsaverage3 (very low polygon count) was created? Best regards, Kai ___ 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] Basename error
If it is not using the basename.m in freesurfer it may fail. Try putting $FREESURFER_HOME/fsfast/toolbox first in your matlab path On 06/22/2014 02:52 PM, Xiaomin Yue wrote: Hi Doug Thanks for you response. The command line is: selxavg3-sess -s subject_0101 -d . -analysis DoD_looming_lh. I checked the basename function in the matlab installed in my computer, which is 2010b. It seems that the basename in the 2010b matlab only accepts one parameter. I tried two ways to avoid the problem. First, I replaced the matlab's basename function with my own basename function. Second, I removed the motion regressor from the analysis.info. The two method indeed avoided the basename function error, but new errors were created as the following: Error using == fmri_hemodyn Too many input argument. Error in == flac_ev2irf at 74 xirf = fmri_hemodync(tirf, delay, tau, alpha); Error in == flac_desmat at 66 [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur); Error in == flac_customize at 356 flacnew = flac_desmat(flacnew); Error in == fast_selxavg3 at 65 flac0=flac_customize(flac0); I suspected that the errors was caused by matlab? if so, what version is required to run 5.3 version correctly? Thanks for your help! Xiaomin Date: Thu, 19 Jun 2014 20:41:28 +0200 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Basename error what is your command line and terminal output On 6/19/14 4:36 PM, Xiaomin Yue wrote: Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using== basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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] low polygon count like fsaverage3
Hi Kai you mean you want to decimate the surface? You can use mris_make_face_parcellation to map something like fsaverage3 to your subject. cheers Bruce On Mon, 23 Jun 2014, Kai Schlamp wrote: Hello again, I am still looking for a way to create a low polygon surface during recon-all (where labels still fit). Is there any (expert) option where I can specify the number of vertices or distance between vertices? How was fsaverage3 (very low polygon count) was created? Best regards, Kai ___ 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] some questions about optseq
I think this is an error I fixed a few months ago. Try this version (for linux) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2 On 06/20/2014 09:05 PM, charujing123 wrote: Hi doug, sorry for not enough information sending to you. optseq2 --ntp 223 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 --tnullmin 2 --tnullmax 8 After running the command above, I get the ex2-001.par and ex2-002.par. In these files, I found that part of NULL window had 10s intervals. However I set the --tnullmax 8, the max time window of NULL should be 8s, not 10s, shouldnot it? Also I check the help of optseq2, and it echo Note: it may not be possible for a given parameter set to keep the NULL stimulus below a certain amount. In this case, the following error message will be printed out 'ERROR: could not enforce tNullMax'. By default, tNullMax is infinite. But I didnot find any ERROR information in the command window. Is that normal? Thanks All the best Rujing Zha 2014-06-21 charujing123 *发 件人：*Douglas Greve gr...@nmr.mgh.harvard.edu *发 送时间：*2014-06-20 23:21 *主 题：*Re: [Freesurfer] some questions about optseq *收 件人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄 送：* weird? I'll need something more specific than that On 6/20/14 4:57 PM, charujing123 wrote: Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. === [psylab16@centos1 ~]$ cat ex1-001.par 0. 2 2.000 1. ev2 2. 0 2.000 1. NULL 4. 1 2.000 1. ev1 6. 0 2.000 1. NULL 8. 1 2.000 1. ev1 10. 0 2.000 1. NULL 12. 1 2.000 1. ev1 14. 0 2.000 1. NULL 16. 1 2.000 1. ev1 18. 0 2.000 1. NULL 20. 2 2.000 1. ev2 22. 0 2.000 1. NULL 24. 1 2.000 1. ev1 26. 0 2.000 1. NULL 28. 1 2.000 1. ev1 30. 0 2.000 1. NULL 32. 2 2.000 1. ev2 34. 0 2.000 1. NULL 36. 2 2.000 1. ev2 38. 0 2.000 1. NULL 40. 2 2.000 1. ev2 42. 0 2.000 1. NULL 44. 2 2.000 1. ev2 46. 0 2.000 1. NULL 48. 1 2.000 1. ev1 50. 0 2.000 1. NULL 52. 2 2.000 1. ev2 54. 0 2.000 1. NULL 56. 1 2.000 1. ev1 58. 0 2.000 1. NULL 60. 2 2.000 1. ev2 62. 0 2.000 1. NULL 64. 2 2.000 1. ev2 66. 0 2.000 1. NULL 68. 1 2.000 1. ev1 70. 0 2.000 1. NULL 72. 1 2.000 1. ev1 74. 0 2.000 1. NULL 76. 1 2.000 1. ev1 78. 0 2.000 1. NULL 80. 2 2.000 1. ev2 82. 0 2.000 1. NULL 84. 2 2.000 1. ev2 86. 0 2.000 1. NULL 88. 2 2.000 1. ev2 90. 0 2.000 1. NULL 92. 1 2.000 1. ev1 94. 0 2.000 1. NULL 96. 1 2.000 1. ev1 98. 0 2.000 1. NULL 100. 1 2.000 1. ev1 102. 0 2.000 1. NULL 104. 2 2.000 1. ev2 106. 0 2.000 1. NULL 108. 1 2.000 1. ev1 110. 0 2.000 1. NULL 112. 1 2.000 1. ev1 114. 0 2.000 1. NULL 116. 2 2.000 1. ev2 118. 0 2.000 1. NULL 120. 1 2.000 1. ev1 122. 0 2.000 1. NULL 124. 2 2.000 1. ev2 126. 0 2.000 1. NULL 128. 2 2.000 1. ev2 130. 0 2.000 1. NULL 132. 2 2.000 1. ev2 134. 0 2.000 1. NULL 136. 1 2.000 1. ev1 138. 0 2.000 1. NULL 140. 2 2.000 1. ev2 142. 0 2.000 1. NULL 144. 2 2.000 1. ev2 146. 0 2.000 1. NULL 148. 2 2.000 1. ev2 150. 0 2.000 1. NULL 152. 2 2.000 1. ev2 154. 0 2.000 1. NULL 156. 1 2.000 1. ev1 158. 0 2.000 1. NULL 160. 2 2.000 1. ev2 162. 0 2.000 1. NULL 164. 2 2.000 1. ev2 166. 0 2.000 1. NULL 168. 1 2.000 1. ev1 170. 0 2.000 1. NULL 172. 2 2.000 1. ev2 174. 0 2.000 1. NULL 176. 1 2.000 1. ev1 178. 0 2.000 1. NULL 180. 2 2.000 1. ev2 182. 0 2.000 1. NULL 184. 2 2.000 1. ev2 186. 0 2.000 1. NULL 188. 1 2.000 1. ev1 190. 0 2.000 1. NULL 192. 1 2.000 1. ev1 194. 0 2.000 1. NULL 196. 1 2.000 1. ev1 198. 0 2.000 1. NULL 200. 1 2.000 1. ev1 202. 0 2.000 1. NULL 204. 2 2.000 1. ev2 206. 0 2.000 1. NULL 208. 2 2.000 1. ev2 210. 0 2.000 1. NULL 212. 2 2.000 1. ev2 214. 0 2.000 1. NULL 216. 1 2.000 1. ev1 218. 0 2.000 1. NULL 220. 1 2.000 1. ev1 222. 0 2.000 1. NULL 224. 1 2.000 1. ev1 226. 0 2.000 1. NULL 228. 1 2.000 1. ev1
Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points
This is a bug in QDEC. I'm surprised it has not surfaced before. It is supposed to be looking in fwhm09 not fwhm9. One work-around is to create a symlink, ie, cd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/ ln -s fwhm09 fwhm9 otherwise, you will have to run mri_glmfit-sim doug On 06/20/2014 11:48 AM, Tudor Popescu wrote: Thanks Doug. After using stage#1 of the longitudinal 2-stage model to create cross-sectional measuers of e.g. thickness change from tp1 to tp2 (e.g. thickness-pc1), I then did analyses in QDEC on these measures to see where in the brain such changes are * different from zero (within each group); and * different between groups (for every pair of groups in the current qdec table, e.g. F vs P) For thickness-pc1 it all went fine, but for area-pc1 analyses, I get this error right after starting the MonteCarlo Null-Z correction: Completed loading of analyzed data. fwhm.dat: 8.654965, rounded to 9. ERROR: CSDread(): could not open /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm9/abs/th13/mc-z.csd. This happens regardless of the threshold used (e.g. 0.01 or 0.05) In case it's relevant, for the thickness analyses (whose correction worked fine), the fwhm.dat was 10.190419, rounded to 11. I am using FS 5.3.0 (Ubuntu). Thanks! Tudor On 17 June 2014 09:29, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It only needs to be accounted for when you compare across all 3 groups, in which case you'd have to use mri_glmfit doug On 6/17/14 12:07 AM, Tudor Popescu wrote: Hi Doug, Thanks... Presumably I'd just leave each possible pair of groups at a time in the qdec table, and delete rows corresponding to subjects of the remaining group? And then do stats on, e.g. long.thickness-rate to compare rate of change between the current pair of groups? Doesn't variability across all 3 groups somehow have to be accounted for? Tudor On 16 June 2014 20:38, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yes, you could do each separately. doug On 6/16/14 8:10 PM, Tudor Popescu wrote: Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of the two-stage model, and I would prefer to run stage#2 (cross-sectional analysis of the difference) with QDEC as opposed to with mri_glmfit. I know that QDEC is meant for 2 groups, but I see that designs with 4 or 6 groups can be analysed with QDEC (as per this https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples FSGD examples page) whereas designs with 3 groups cannot be. It seems to me that an even number of groups is QDEC-able while an odd number isn't, but is there any workaround so that I can still use QDEC? Perhaps if I only do pairwise comparisons one at a time, i.e. treatment1 vs control and treatment2 vs control? Many thanks! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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
Re: [Freesurfer] Group analysis over different studies?
Sorry, yes, I meant ces instead of gamma. It is not set up to use CVS. On my todo list... On 06/17/2014 03:13 PM, Terri Scott wrote: Hi Doug, Is gamma.mgh the same as ces.nii.gz? I'm working with data processed with an older version of Freesurfer, not exactly sure which. I have a related question also; the masks and meanfunc images don't seem to be lining up that well after running isxconcat-sess. Would is be possible for me to use cvs normalization on these data before concatenating within each study? I have run the cvs transformations already, but I'm not sure how I would chose which functional data to apply them to, and if I'd need to set up a new filesystem for the normalized data. Thanks again! Terri On Tue, Jun 17, 2014 at 4:27 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Just run isxconcat-sess for each study, then mri_concat study1/gamma.mgh study2/gamma.mgh --o study1-and-study2-gamma.mgh then run mri_glmfit on the above output doug On 6/16/14 11:54 PM, Terri Scott wrote: Hi all, I want to do a group analysis using subjects that were run in different studies but who have (some of) the same relevant functional contrasts. Is there a way to run something like isxconcat-sess on data from different analysis streams? Or if not, which files do I need to collect and align from each subject in order to run mri_glmfit? What would be the best way to handle this analysis? Thanks, Terri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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] Project probabilistic connectivity maps to pial and calculate mass center
I'm not sure all that you are trying to do, but if you have a registration that maps to the orig.mgz, then you can use mri_vol2surf to map to the pial surface. Run it with --help to get more info doug On 06/20/2014 12:26 AM, gong jinnan wrote: Dear all, I have used probabilistic tractography methods by FSL-FDT to get probabilistic connectivity between grey-white matter interface of precentral and basal ganglia in subjects’ space. The latter one was used as classification mask. And then all of tractography maps were registered to MNI space. Now I want to project tractography results like seed_to_BG.nii.gz to pial in Freesurfer and calculate mass center of those maps. But unfortunately I am not clear how to do that. So there is my question: 1.It is not difficult to project seed_to_BG.nii.gz to .../mri/orig.mgz. But how to project to pial after that? 2.How can I get mass center like pictures in attachment. I tried calculated mass center of seed_to_BG.nii.gz in MNI space, but the mass center point does not fall in precentral. So I want to do that in pial. 3.How to transform subjects’ pial to talairach pial? I searched method to do that for a long time, but have no idea yet. So I hope I can get valuable suggestions here. I will be grateful if you can help me! Sincerely， Jinnan Gong Best wishes for you! Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China ___ 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] Labels to annotation
Don't use FreeSurferColorLUT.txt, you need to create your own color table whose format is like FreeSurferColorLUT.txt doug On 06/20/2014 03:49 AM, Karen Marie Sandø Ambrosen wrote: Hi Bruce, When I input all the labels in the mris_label2annot command I get the result shown in: H09_copy_AllLabels2annot.png and it gives a lot of warnings: Warning: vertex 142382 with annotation - out of range!. The command I use looks like: mris_label2annot --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l label1 --l label2 ... --labeln --s H09_copy --a output_annotation --h lh When I run the command I get a lot of warnings: WARNING: vertex 139930 maps to multiple labels! (overwriting). In comparison if I create an annotation using only, e.g., the first 10 labels I get the result shown in: H09_copy_10Labels2annot.png and I don't get any warnings. If I create an annotation using the first 100 labels I get the result shown in: H09_copy_100Labels2annot.png and I get warnings similar to when I use all the labels. I hope this makes the problem more clear. Best, Karen On 06/20/2014 04:02 AM, Bruce Fischl wrote: Hi Karen What do you mean the results don't look right? Can you send an image? Cheers Bruce On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen k...@dtu.dk wrote: Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: WARNING: vertex 6021 maps to multiple labels! (overwriting), and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels--surface labels--annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen ___ 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 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] How to extract significant result for each subject
If you run mri_glmfit-sim, it will extract this for you. Run it with --help to get more information doug On 06/12/2014 10:53 PM, kangchengwang0...@gmail.com wrote: Dear freesurfers, I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this? Thank you Wang Kangcheng ( New learner of freesurfer ) ___ 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 to volume visualization
Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format. Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible. I'm wondering whether any one has a better idea for this? Thanks James ___ 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] Vertex analysis cluster values
Hi Rachel, are you saying that there does not seem to be an effect in the mean using the same contrast that was used to compute the clusters? How are you doing the test in the mean? Are you sure you have the same design and contrast matrices? doug On 06/06/2014 02:38 PM, Rachel Jonas wrote: Hi Freesurfer users, I ran a GLM vertex analysis testing an interaction between group and a task measure, and a few clusters popped up that survived correction. I extracted the mean thickness values at the clusters (using cache.th13.abs.y.ocn.dat) in order to plot these interactions in graph form. When I did this, the interactions look nonexistent, and there doesn't appear to be any relationships between my task measure and thickness in either group. My FSGD file contains 4 groups (patients controls with two different scanner sites), and my continuous variables are age and this task measure. I only have 15 patients and 15 controls, so my only thought so far is that my power is low, and these results are spurious. My contrast file is: 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 Any insight would be greatly appreciated! Thank you! Rachel ___ 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] Edits, where art thou?
Hi! When I edit my data, for instance wm editing, I do not see the changes applied to the original image. To make you understand what I do: Open up freeview, load the image, Wm and brainmask, with wm at the top. Then I go into voxel edit, press recon edit, and start filling in topographical defects and do some wm editing. HOWEVER, after I run recon all (recon-all -autorecon2 -autorecon3 -subjid anon)and it's finished without problems, I do not see the edits done on my image. Sure, I see the yellow colour which I filled some spots with, but I was thinking that I would see an edited image, that is with pia (topographical defects) and wm surface going out to the areas I edited. Not only yellow filling which was there before since I edited. Am I doing something wrong? Is the reconprocessed images hidden out there somewhere? Freesurfer team, please help! Best, MAX ___ 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] recon-all ERROR, no idea why
hello, freesurfers, Im having trouble using recon-all, I tried the prebuilt virtual machine and a fresh unbuntu install without luck. Would anyone have a look at my recon-all.log? I cant spot any error. *Thanks * *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net http://www.NeuralControl.net* Mon Jun 23 11:35:42 EDT 2014 /media/sf_Imagery/FreeSurfer/xx /usr/local/freesurfer/bin/recon-all -i /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img1.dcm -subjid xx -sd /media/sf_Imagery/FreeSurfer -all subjid xx setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28136 maxlocks unlimited maxsignal28136 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 3616064 6924002923664 0 94528 405020 -/+ buffers/cache: 1928523423212 Swap: 1944572 01944572 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register
Re: [Freesurfer] Why the result was not same for the same subject
Wang, what command-line flags were included? can you send me the recon-all.log file for these runs? The results should be the same with repeated runs if the default flags were used. Nick On Jun 21, 2014, at 10:20 PM, wangkangcheng_gmail kangchengwang0...@gmail.com wrote: Dear Bruce Yes. The following is an example result for the subject (The id from Sub_1 to Sub_10 is the same subject) that I calculate ten times. rh.aparc.a2009s.volume rh_G_and_S_frontomargin_volume Sub_1 1713 Sub_2 1950 Sub_3 1789 Sub_4 1783 Sub_5 1879 Sub_6 1778 Sub_7 1892 Sub_8 1782 Sub_9 1799 Sub_101799 Thank you Wang Kangcheng ___ 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] recon-all ERROR, no idea why
can you run the command below and send nu.log? cd /media/sf_Imagery/FreeSurfer/xx/mri mri_nu_correct.mni --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz | tee nu.log On 06/23/2014 11:49 AM, Remy Wahnoun wrote: hello, freesurfers, Im having trouble using recon-all, I tried the prebuilt virtual machine and a fresh unbuntu install without luck. Would anyone have a look at my recon-all.log? I cant spot any error. /Thanks / / / *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University /www.NeuralControl.net http://www.NeuralControl.net/ Mon Jun 23 11:35:42 EDT 2014 /media/sf_Imagery/FreeSurfer/xx /usr/local/freesurfer/bin/recon-all -i /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img1.dcm -subjid xx -sd /media/sf_Imagery/FreeSurfer -all subjid xx setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28136 maxlocks unlimited maxsignal28136 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free shared buffers cached Mem: 3616064 6924002923664 094528 405020 -/+ buffers/cache: 1928523423212 Swap: 1944572 01944572 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400
Re: [Freesurfer] Retinotopic mapping using selxavg3-sess
Yes, I've installed FSL already. I can launch FSL by typing fslview in the command window. However, it seems that the $FSLDIR is not defined. Should I define it manually using setenv before running selxavg3-sess? -- Alan Lee sites.google.com/site/alanlflee/ On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Do you have FSL installed? If so, what is your $FSLDIR? On 06/19/2014 03:03 PM, Alan Lee wrote: Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it. Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/ On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It looks for it in the current folder. You must run this from the same folder you ran mkanalysis-sess from (which should be your project folder) On 6/17/14 4:13 PM, Alan Lee wrote: Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 3): selxavg3-sess -a Retinotopy.3.lh -s 3 I got the following message: ERROR: /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does not exist It seems to look for a Retintopy folder within /Retinotopy/3/. I suppose the Retinotopy folder should be placed under freesurfer/subjects/ ? Am I missing something here? Any help would be greatly appreciated. Many thanks, Alan = debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess -a Retinotopy.3.lh -s 3 Surface data self lh -- selxavg3-sess logfile is /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.3.lh-140617154401.log -- preproc-sess -s 3 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.3.lh -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ root setenv FREESURFER_HOME /usr/local/freesurfer/ setenv
Re: [Freesurfer] Retinotopic mapping using selxavg3-sess
Yes. I'm surprised that FSL would run at all without that defined. doug On 06/23/2014 12:44 PM, Alan Lee wrote: Yes, I've installed FSL already. I can launch FSL by typing fslview in the command window. However, it seems that the $FSLDIR is not defined. Should I define it manually using setenv before running selxavg3-sess? -- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/ On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Do you have FSL installed? If so, what is your $FSLDIR? On 06/19/2014 03:03 PM, Alan Lee wrote: Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it. Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/ On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It looks for it in the current folder. You must run this from the same folder you ran mkanalysis-sess from (which should be your project folder) On 6/17/14 4:13 PM, Alan Lee wrote: Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 3): selxavg3-sess -a Retinotopy.3.lh -s 3 I got the following message: ERROR: /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does not exist It seems to look for a Retintopy folder within /Retinotopy/3/. I suppose the Retinotopy folder should be placed under freesurfer/subjects/ ? Am I missing something here? Any help would be greatly appreciated. Many thanks, Alan = debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess -a
[Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint
Hi, I'm attempting to do some longitudinal processing on a set of data with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months after Final. When visually checking over a subject in Freeview, I notice that all of my Midpoint runs are left-right flipped, where the other 3 timepoints' scans are congruent with one another. What can I do to flip these Midpoint volumes left-right before I rerun them all in recon-all -all? As well, since these are going to the same subjects for my longitudinal design in creating a 'base' file we have to ensure that we maintain the same orientation of the brain across all timepoints (left-right)? Thanks in advance, - Bryan ___ 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] Correcting left-right flip for multiple subjects at the same timepoint
How did you convert to mgz? Did you start with dicoms and use mri_convert? How do you know they are flipped? On 06/23/2014 12:56 PM, Chiu, Bryan (PHTH) wrote: Hi, I'm attempting to do some longitudinal processing on a set of data with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months after Final. When visually checking over a subject in Freeview, I notice that all of my Midpoint runs are left-right flipped, where the other 3 timepoints' scans are congruent with one another. What can I do to flip these Midpoint volumes left-right before I rerun them all in recon-all -all? As well, since these are going to the same subjects for my longitudinal design in creating a 'base' file we have to ensure that we maintain the same orientation of the brain across all timepoints (left-right)? Thanks in advance, - Bryan ___ 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] A comparison between atlases
Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? ___ 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] Fwd: surface to volume visualization
Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format. Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible. I'm wondering whether any one has a better idea for this? Thanks James ___ 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] Why the result was not same for the same subject
There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainly suggest reading the paper titled: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain - Bryan ___ 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] Extracting mean diffusivity values from diffusion data in freesurfer 5.3
Was this ever answered? 1. Units - Not sure what the units of MD are. It might depend on your b-value 2. MD is not constrained to be between 0 and 1. Where are you getting that? 3. I don't know about the CC values. The CC ROIs are pretty small, and you might be getting significant partial voluming doug On 06/06/2014 02:06 AM, Rotem Saar wrote: Dear freesurfer experts, I'm using freesurfer 5.3 for extracting FA and MD values for each region from the *aseg file for each subject. While I get validated FA values (I validated them with you, the literature and some other software I used), I have a problem getting reasonable MD values. This is the script I'm using for extracting the MD values: 1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec 2) mri_label2vol --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz 3) mri_segstats --seg-erode 1 --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked It writes *.txt files similar to the ones of the FA (and also the volumetric analysis) which is good, but - 1) I can't understand the units (it is written unknown). can u tell me what do these units refer to ? 2) I can't understand why the units I get don't corresponds to the units in the literature (0-1). Is there a transformation I need to apply to these units in order to get the values we all see in the literature (MD values ranges between 0 to 1 in the papers I read). 3) I am concerned about the differences in the values both between and within subjects. For example, see 3 different subjects and their MD values for the corpus-callosum: subject 1: 35 251 368 368.0 CC_Posterior 7.4783 7.9938 0.16.16. 36 252 110 110.0 CC_Mid_Posterior 56.7273 476.3758 0. 5002. 5002. 37 253 205 205.0 CC_Central 992.4537 1806.8883 0. 5002. 5002. 38 254 132 132.0 CC_Mid_Anterior 1664.2954 2328.8467 43. 5002. 4959. 39 255 277 277.0 CC_Anterior 1723.4620 1914.7883 0. 5002. 5002. subject 2: 36 251 328 328.0 CC_Posterior 0. 0. 0. 0. 0. 37 25278 78.0 CC_Mid_Posterior 43.9744 226.6371 0. 2000. 2000. 38 253 100 100.0 CC_Central 203.0800 779.8602 0. 5001. 5001. 39 25483 83.0 CC_Mid_Anterior 264.5783 364.1581 0. 1002. 1002. 40 255 321 321.0 CC_Anterior 985.8879 720.5300 0. 3028. 3028. subject 3: 35 251 424 424.0 CC_Posterior 20.6840 6.6236 10.60.50. 36 252 160 160.0 CC_Mid_Posterior 143.4312 780.4187 0. 5001. 5001. 37 253 202 202.0 CC_Central 538.0248 1143.9441 0. 5001. 5001. 38 254 179 179.0 CC_Mid_Anterior 496.5140 623.4088 0. 2023. 2023. 39 255 361 361.0 CC_Anterior 211.6094 539.0007 0. 2028. 2028. the values are really different both within the CC parts of the same subject (does this make any sense ??) and also between subjects... We ruled out a problem in the gradient matrix (both with you and because the FA values corresponds to reasonable values both from the literature and other software we use). Can u please advise on how can we solve this issue ? We are in the middle of submission of a very novel study and were required to show addition analysis of the MD values - this is why this is so impotent to us. Attached please find the full *.txt files I got. Thanks for your help. Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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:
Re: [Freesurfer] A comparison between atlases
Hi Dorian you don't need to combine them in any specific way if all you want is to look at ROI-based stats. Just take the ones from each atlas that you like. cheers Bruce On Mon, 23 Jun 2014, Dorian P. wrote: Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? ___ 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] Fwd: surface to volume visualization
Hi James Ruopeng is traveling and may not answer quickly, although Louis might be able to help Bruce On Mon, 23 Jun 2014, james pardon wrote: Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format. Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible. I'm wondering whether any one has a better idea for this? Thanks James ___ 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] Why the result was not same for the same subject
Actually, if you run 'recon-all' a second time (from scratch) on the same subject, on the same platform/architecture, and you use the default recon-all settings (i.e., don't use the -randomness flag, or specify your random seed via the -rng-seed flag), then you should get identical results, because for quite a few versions now, recon-all has been set up to use the same random seed (1234) in all the binaries that involve randomness. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 6/23/14 12:05 PM, Chiu, Bryan (PHTH) bryan.c...@ubc.ca wrote: There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainly suggest reading the paper titled: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain - Bryan ___ 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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
Re: [Freesurfer] A comparison between atlases
For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? Not by default, bu you can create one easily enough with cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz doug On 06/23/2014 01:03 PM, Dorian P. wrote: Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? ___ 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] Why the result was not same for the same subject
yes, that was our goal some time ago and we thought we had succeeded in tracking down and fixing any randomness if the same seed is specified Bruce On Mon, 23 Jun 2014, Harms, Michael wrote: Actually, if you run 'recon-all' a second time (from scratch) on the same subject, on the same platform/architecture, and you use the default recon-all settings (i.e., don't use the -randomness flag, or specify your random seed via the -rng-seed flag), then you should get identical results, because for quite a few versions now, recon-all has been set up to use the same random seed (1234) in all the binaries that involve randomness. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 6/23/14 12:05 PM, Chiu, Bryan (PHTH) bryan.c...@ubc.ca wrote: There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainly suggest reading the paper titled: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain - Bryan ___ 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC Error loading the data table
Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview However, when I try to load my data table it returns the error. Loading data table /home/pcopy_project/qdec/qdec.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 57 Reading discrete factor levels from config file /home/pcopy_project/qdec/gender.levels Female Male done. Reading discrete factor levels from config file /home/pcopy_project/qdec/diagnosis.levels Control Disease done. ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column INFO: If 'gender' is a discrete factor, then create a file named 'gender.levels' containing the valid factor names one per line. Error loading the data table. As you see I have a 'gender.levels' file in the same directory as the data file and it reads it above. I still get the error. I am new to QDEC and any help would be appreciated. Thank you Mohammed Goryawala, PhD Research Associate Department of Radiology University of Miami Miller School 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.
Re: [Freesurfer] A comparison between atlases
Thank you Bruce and Douglas, I meant to combine them because I did not want overlaps. Can I advance one more question as we are here. How can I get an average thickness of the entire lateral temporal lobe (inferior, medial, temporal gyri)? The average of the three gyri may not be useful as one gyrus may be bigger and should be counted accordingly in the average thickness of the entire lateral part. Thank you. 2014-06-23 13:22 GMT-04:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? Not by default, bu you can create one easily enough with cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz doug On 06/23/2014 01:03 PM, Dorian P. wrote: Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? ___ 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 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] QDEC Error loading the data table
That does look pretty silly. How did you create your qdec.table.dat and level files? If you created them under windows, then that could be the problem. If not, post your qdec.table.dat file and the gender.level file and I'll take a look On 06/23/2014 01:33 PM, Mohammed Goryawala wrote: Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview However, when I try to load my data table it returns the error. Loading data table /home/pcopy_project/qdec/qdec.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 57 Reading discrete factor levels from config file /home/pcopy_project/qdec/gender.levels Female Male done. Reading discrete factor levels from config file /home/pcopy_project/qdec/diagnosis.levels Control Disease done. ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column INFO: If 'gender' is a discrete factor, then create a file named 'gender.levels' containing the valid factor names one per line. Error loading the data table. As you see I have a 'gender.levels' file in the same directory as the data file and it reads it above. I still get the error. I am new to QDEC and any help would be appreciated. Thank you Mohammed Goryawala, PhD Research Associate Department of Radiology University of Miami Miller School of Medicine ___ 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] A comparison between atlases
On 06/23/2014 01:35 PM, Dorian P. wrote: Thank you Bruce and Douglas, I meant to combine them because I did not want overlaps. I don't think we have any tools to mix and match them. Can I advance one more question as we are here. How can I get an average thickness of the entire lateral temporal lobe (inferior, medial, temporal gyri)? The average of the three gyri may not be useful as one gyrus may be bigger and should be counted accordingly in the average thickness of the entire lateral part. You can create a new annotation of the major lobes with mri_annotation2label --subject $subject --hemi $hemi --lobesStrict lobes This creates ?h.lobes.annot doug Thank you. 2014-06-23 13:22 GMT-04:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? Not by default, bu you can create one easily enough with cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz doug On 06/23/2014 01:03 PM, Dorian P. wrote: Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 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 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
[Freesurfer] RAS to voxel transform
Hi, I'm trying to understand the conversion from RAS (freesurfer surface coordinate) to volume space (x, y, and z.. According to Graham Wideman documentation here http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not outdated), Right is negative x, *Anterior is positive z*, and *Superior is positive y*. Just to double check, usign mri_info on a sample T1.mgz in one subject I get this ras to voxel transform: -1 00 126.944 0 0 -1 135.16 0 10 110.6 0 001 Assuming we have correctly set the (0, 0, 0), and we can extract R A and S (respectively) coordinates using C++ or Python code it means: Right is negative x, *Anterior is negative z*, and *Superior is positive y* (conflicting coordinates are in vold). Am I missing anything here, or coordinate systems have changed from the probably outdated documentation? Thanks in advance for any input on this rather confusing point. All the best, Arman ___ 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] QDEC Error loading the data table
Hi Doug, I did create them in windows. I will recreate them on the linux machine and carry out the processing. Thanks for the help. Mohammed On Mon, Jun 23, 2014 at 1:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: That does look pretty silly. How did you create your qdec.table.dat and level files? If you created them under windows, then that could be the problem. If not, post your qdec.table.dat file and the gender.level file and I'll take a look On 06/23/2014 01:33 PM, Mohammed Goryawala wrote: Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview However, when I try to load my data table it returns the error. Loading data table /home/pcopy_project/qdec/qdec.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 57 Reading discrete factor levels from config file /home/pcopy_project/qdec/gender.levels Female Male done. Reading discrete factor levels from config file /home/pcopy_project/qdec/diagnosis.levels Control Disease done. ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column INFO: If 'gender' is a discrete factor, then create a file named 'gender.levels' containing the valid factor names one per line. Error loading the data table. As you see I have a 'gender.levels' file in the same directory as the data file and it reads it above. I still get the error. I am new to QDEC and any help would be appreciated. Thank you Mohammed Goryawala, PhD Research Associate Department of Radiology University of Miami Miller School of Medicine ___ 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 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] RAS to voxel transform
Your interpretation is not correct. RAS always means that R is pos x, A is pos y, and S is pos z. That is the voxel-to-RAS transform. Here voxel means column-row-slice. So this matrix takes a col, row, slice and converts it into a RAS. So that first negative 1 means that as the column number increases the R decreases (ie, becomes more leftward) Look at our wiki http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for more info doug On 06/23/2014 01:44 PM, Arman Eshaghi wrote: Hi, I'm trying to understand the conversion from RAS (freesurfer surface coordinate) to volume space (x, y, and z.. According to Graham Wideman documentation here http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not outdated), Right is negative x, *Anterior is positive z*, and *Superior is positive y*. Just to double check, usign mri_info on a sample T1.mgz in one subject I get this ras to voxel transform: -1 00 126.944 0 0 -1 135.16 0 10 110.6 0 001 Assuming we have correctly set the (0, 0, 0), and we can extract R A and S (respectively) coordinates using C++ or Python code it means: Right is negative x, *Anterior is negative z*, and *Superior is positive y* (conflicting coordinates are in vold). Am I missing anything here, or coordinate systems have changed from the probably outdated documentation? Thanks in advance for any input on this rather confusing point. All the best, Arman ___ 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] hippocampal subfields in young subjects
Dear Koen and Freesurfers, I haven't receive any further replies regarding the black lines surrounding the subfields I found in the sample of subjects I am analyzing. As I said the subjects are quite young (9-14 years of age) and I visualized the subfields with Freeview. Do you have any idea why this is happening? This does mean the GEMS tool should not be applied in such young subjects? Any help would be greatly appreciated! Many thanks, joana 2014-06-13 15:40 GMT+02:00 Joana Braga Pereira jbragapere...@gmail.com: Hi Koen, Thanks for such a prompt reply. I visualized it in freeview with: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt Thanks, Joana 2014-06-13 15:23 GMT+02:00 Koen Van Leemput k...@nmr.mgh.harvard.edu: Hi Joana, This looks like a visualization issue rather than a segmentation error to me. How did you visualize this? Koen On Jun 13, 2014 2:59 PM, Joana Braga Pereira jbragapere...@gmail.com wrote: Dear all, I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of hippocampal subfields in subjects between 9 and 14 years of age with 3T T1-weighted MRI scans. I noticed that a blackline is consistently drawn around the surface of the subfields (see attached figure) and was wondering whether this is normal. Since the tool has not been validated in young subjects I would like to know if the black line observed in the figure shows that the segmentation has not been carried out correctly. Any help will be greatly appreciated. Many thanks, Joana ___ 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 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 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] recon-all ERROR, no idea why
Thanks Douglas,
I definitely appreciate your help.
Here is what it Spit out,
*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
*www.NeuralControl.net http://www.neuralcontrol.net/*
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 1
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --proto-iters
shift
switch ( $flag )
switch ( --proto-iters )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set nProtoIters = $argv[1] ; shift ;
set nProtoIters = 1000
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --distance
shift
switch ( $flag )
switch ( --distance )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set Distance = $argv[1] ; shift ;
set Distance = 50
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --no-rescale
shift
switch ( $flag )
switch ( --no-rescale )
set DoRescale = 0 ;
set DoRescale = 0
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = orig_nu.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname orig_nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log
./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/usr/local/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
tee -a ./mri_nu_correct.mni.log
--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz
--o orig_nu.mgz
echo nIters $nIters | tee -a $LF
echo nIters 1
tee -a ./mri_nu_correct.mni.log
nIters 1
echo $VERSION | tee -a $LF
tee -a ./mri_nu_correct.mni.log
echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48
UTC 2014 i686 i686 i386 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
Mon Jun 23 15:32:45 EDT 2014
nu_correct -version | tee -a $LF
nu_correct -version
tee -a ./mri_nu_correct.mni.log
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu)
on 2010-02-20 at 20:19:13
if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
set tmpdir = ./tmp.mri_nu_correct.mni.1745
mkdir -p $tmpdir
mkdir -p ./tmp.mri_nu_correct.mni.1745
echo tmpdir is $tmpdir | tee -a $LF
echo tmpdir is ./tmp.mri_nu_correct.mni.1745
tee -a ./mri_nu_correct.mni.log
tmpdir is ./tmp.mri_nu_correct.mni.1745
set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )
if ( $UseFloat ) set cmd = ( $cmd -odt float )
if ( 1 ) set cmd = ( mri_convert orig.mgz
./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float )
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
echo $cmd | tee -a $LF
[Freesurfer] fMRI Image Acquisition and Analyses Course : October 16-18, 2014 (fwd)
FYI -- The Mind Research Network (MIND) is pleased to invite you to the fMRI Image Acquisition and Analyses Course held on October 16-18, 2014 on the campus of the University of New Mexico in Albuquerque, New Mexico. For more information and registration, see http://www.mrn.org/education-outreach/courses-and-events/ Special topics include the unique issues that multiband EPI (i.e., whole brain subsecond EPI) brings to fMRI analyses ***Email Kent A. Kiehl kki...@unm.edu or fmricou...@mrn.org with any questions. We hope to see you there. Thanks for your time, and have a great day! ___ 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] problem with qdec stats tables
Dear mailing-list, Ive got a question concerning the file types of stats tables in qdec. After generating the stats tables there are two files e.g. lh.aparc.a2005s.area.stats and lh.aparc.area.stats. Which one is the right one to work with ( statistical analysis)? How do they differ in characteristics and values? Thanks, best regards, Kristina ___ 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] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log
Nick, Thanks for your kind help. I uploaded my orig.mgz i.e. 001.mgz using Martinos center file drop. Thanks Venkat On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Venkat, Can you send me your orig.mgz so that I can attempt to replicate? Nick On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote: Hi Bruce, Thanks very much. I will wait for Avi Synder's response. Thanks a lot Venkat On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Venkat I'll cc Avi Snyder. Avi: do you know what this error message means? thanks Bruce On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I am sorry to post this again. Any help will be greatly appreciated. I am struck as I am unable to run the recon-all step. Thanks Venkat -- Forwarded message -- From: Venkateswaran Rajagopalan venkateswa...@hyderabad.bits-pilani.ac.in Date: Fri, Jun 20, 2014 at 5:14 PM Subject: mpr2mni305 failed, see transforms/talairach_avi.log To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr
