[Freesurfer] Fwd: visualizing paths stats by voxel
> Begin forwarded message: > > From: Janosch Linkersdörfer > Subject: Re: visualizing paths stats by voxel > Date: 3 Nov 2015 09:37:48 CET > To: Anastasia Yendiki > Cc: freesurfer@nmr.mgh.harvard.edu > > Hi Anastasia and list, > > sorry, I just now got around to testing out the new build of dmri_paths you > sent me. Sadly, the results look about the same: > > > > Here the path stats file for the left SLFt: #!ascii label 53 1 -50.1205 2.05458 20.1324 0 2 -49.0568 1.40645 20.8743 0 3 -47.024 0.495407 22.0052 0 4 -46.0977 -0.262421 22.1583 0 5 -44.4218 -1.30921 22.7764 0 6 -43.2968 -1.3833 23.3134 0 7 -41.2815 -1.94728 24.0532 0 8 -40.1774 -2.62188 24.8471 0 9 -39.143 -3.68113 25.4572 0 10 -38.0383 -4.9254 26.3159 0 11 -37.2828 -6.68602 27.0788 0 12 -36.5155 -8.22572 27.6033 0 13 -35.7584 -10.1152 28.2235 0 14 -35.3687 -11.6727 28.7698 0 15 -34.7487 -13.5948 29.3084 0 16 -34.0861 -15.8398 29.7752 0 17 -33.9133 -17.4602 30.2452 0 18 -33.5104 -19.6399 30.5545 0 19 -33.3487 -21.7044 30.7416 0 20 -32.9916 -23.9215 30.9002 0 21 -31.4122 -26.7961 31.088 0 22 -31.2762 -28.9119 31.2611 0 23 -31.1289 -31.2752 30.8061 0 24 -30.8814 -33.1307 30.5293 0 25 -29.5803 -36.1004 30.7024 0 26 -27.2789 -39.691 31.0453 0 27 -16.641 -48.8283 35.0155 0 28 -16.5297 -49.7169 34.264 0 29 -16.5432 -50.9074 32.951 0 30 -16.7235 -51.6755 31.9552 0 31 -16.9983 -52.2055 30.3891 0 32 -17.3004 -52.6851 28.9923 0 33 -17.6197 -53.0619 27.5988 0 34 -17.9982 -53.2888 26.4068 0 35 -18.4567 -53.4429 25.1512 0 36 -18.9968 -53.6854 23.6134 0 37 -19.8229 -53.7862 21.8063 0 38 -20.4389 -54.1143 20.5701 0 39 -21.1905 -54.2719 19.3752 0 40 -21.7858 -54.4113 18.3986 0 41 -23.0093 -54.3412 16.9705 0 42 -24.1073 -54.5756 15.7345 0 43 -25.302 -54.5493 14.8829 0 44 -26.706 -54.7199 13.7208 0 45 -27.1493 -55.0881 13.003 0 46 -28.5131 -55.2495 12.4195 0 47 -25.8897 -58.0703 15.0856 0 48 -22.3874 -60.6226 18.735 0 49 -14.1178 -65.6153 25.9802 0 50 -9.17648 -68.7466 30.4727 0 51 3.31329 -77.2664 41.7526 0 52 22.0756 -89.6051 55.8685 0 53 19.4398 -88.1799 54.2416 0 > > > What could be the problem?! I think I did what you suggested: > > - install the new version of dmri_paths > (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it > executable > - rerun trac-all -path for the subjects with only one time point > - rerun trac-all -stat for all subjects > > Also: Is that problem only a visualization problem, or does it also mean that > the values I get for a participant at a specific part of a tract are not > aligned and I cannot analyze the data in that way? > > Thanks for your help!! > > Best, > > Janosch > > >> On 20 Aug 2015, at 21:35, Anastasia Yendiki >> wrote: >> >> >> Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of >> dmri_paths tomorrow. You'll have to replace your copy of >> $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only >> for the subjects that have 1 time point. Then rerun "trac-all -stat" with >> all subjects together. And then tell us what other problem you find :) >> >> Best, >> a.y >> >> On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: >> >>> Hey Anastasia, >>> >>>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki >>>> : >>>> >>>> >>>> Hi Janosch - There is a bug in how the output paths are saved when >>>> longitudinal TRACULA is run with one time point only. I'm working on a fix. >>> >>> OK, then I'm relieved that it isn't an error on my side. Thank you very >>> much for looking into it! >>> >>>> In the meantime, you can try your analysis with the subjects that have >>>> multiple time points and you won't be affected by this problem. I can see >>>> that the subjects with a single time point are about 1/3 of your sample, >>>> and so you may not want to drop them completely. >>> >>> Yeah, it's children's data, so I'm happy about every measurement we got. >>> I'll be waiting for the fixed script to be able to include all subjects in >>> the analysis... >>> >>>> >>>> Thank you for trying things that nobody else has tried and finding these >>>> bugs! >>> >>> Somebody has to be the first, eh? :) >>> >>> Thank you very much, >>> >>> Janosch >>> >>>> >>>> More soon, >>>> a.y >>>> >>>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: >>>> >>>>> Hey Anastasia
Re: [Freesurfer] visualizing paths stats by voxel
Hi Anastasia and list, sorry, I just now got around to testing out the new build of dmri_paths you sent me. Sadly, the results look about the same: Here the path stats file for the left SLFt: #!ascii label 53 1 -50.1205 2.05458 20.1324 0 2 -49.0568 1.40645 20.8743 0 3 -47.024 0.495407 22.0052 0 4 -46.0977 -0.262421 22.1583 0 5 -44.4218 -1.30921 22.7764 0 6 -43.2968 -1.3833 23.3134 0 7 -41.2815 -1.94728 24.0532 0 8 -40.1774 -2.62188 24.8471 0 9 -39.143 -3.68113 25.4572 0 10 -38.0383 -4.9254 26.3159 0 11 -37.2828 -6.68602 27.0788 0 12 -36.5155 -8.22572 27.6033 0 13 -35.7584 -10.1152 28.2235 0 14 -35.3687 -11.6727 28.7698 0 15 -34.7487 -13.5948 29.3084 0 16 -34.0861 -15.8398 29.7752 0 17 -33.9133 -17.4602 30.2452 0 18 -33.5104 -19.6399 30.5545 0 19 -33.3487 -21.7044 30.7416 0 20 -32.9916 -23.9215 30.9002 0 21 -31.4122 -26.7961 31.088 0 22 -31.2762 -28.9119 31.2611 0 23 -31.1289 -31.2752 30.8061 0 24 -30.8814 -33.1307 30.5293 0 25 -29.5803 -36.1004 30.7024 0 26 -27.2789 -39.691 31.0453 0 27 -16.641 -48.8283 35.0155 0 28 -16.5297 -49.7169 34.264 0 29 -16.5432 -50.9074 32.951 0 30 -16.7235 -51.6755 31.9552 0 31 -16.9983 -52.2055 30.3891 0 32 -17.3004 -52.6851 28.9923 0 33 -17.6197 -53.0619 27.5988 0 34 -17.9982 -53.2888 26.4068 0 35 -18.4567 -53.4429 25.1512 0 36 -18.9968 -53.6854 23.6134 0 37 -19.8229 -53.7862 21.8063 0 38 -20.4389 -54.1143 20.5701 0 39 -21.1905 -54.2719 19.3752 0 40 -21.7858 -54.4113 18.3986 0 41 -23.0093 -54.3412 16.9705 0 42 -24.1073 -54.5756 15.7345 0 43 -25.302 -54.5493 14.8829 0 44 -26.706 -54.7199 13.7208 0 45 -27.1493 -55.0881 13.003 0 46 -28.5131 -55.2495 12.4195 0 47 -25.8897 -58.0703 15.0856 0 48 -22.3874 -60.6226 18.735 0 49 -14.1178 -65.6153 25.9802 0 50 -9.17648 -68.7466 30.4727 0 51 3.31329 -77.2664 41.7526 0 52 22.0756 -89.6051 55.8685 0 53 19.4398 -88.1799 54.2416 0 What could be the problem?! I think I did what you suggested: - install the new version of dmri_paths (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it executable - rerun trac-all -path for the subjects with only one time point - rerun trac-all -stat for all subjects Also: Is that problem only a visualization problem, or does it also mean that the values I get for a participant at a specific part of a tract are not aligned and I cannot analyze the data in that way? Thanks for your help!! Best, Janosch > On 20 Aug 2015, at 21:35, Anastasia Yendiki > wrote: > > > Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of > dmri_paths tomorrow. You'll have to replace your copy of > $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only > for the subjects that have 1 time point. Then rerun "trac-all -stat" with all > subjects together. And then tell us what other problem you find :) > > Best, > a.y > > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: > >> Hey Anastasia, >> >>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki >>> : >>> >>> >>> Hi Janosch - There is a bug in how the output paths are saved when >>> longitudinal TRACULA is run with one time point only. I'm working on a fix. >> >> OK, then I'm relieved that it isn't an error on my side. Thank you very much >> for looking into it! >> >>> In the meantime, you can try your analysis with the subjects that have >>> multiple time points and you won't be affected by this problem. I can see >>> that the subjects with a single time point are about 1/3 of your sample, >>> and so you may not want to drop them completely. >> >> Yeah, it's children's data, so I'm happy about every measurement we got. >> I'll be waiting for the fixed script to be able to include all subjects in >> the analysis... >> >>> >>> Thank you for trying things that nobody else has tried and finding these >>> bugs! >> >> Somebody has to be the first, eh? :) >> >> Thank you very much, >> >> Janosch >> >>> >>> More soon, >>> a.y >>> >>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: >>> >>>> Hey Anastasia, >>>> >>>> thanks for looking into this. >>>> >>>>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki >>>>> : >>>>> >>>>> >>>>> Hi Janosch - Looking at the stats files of your subjects, just by a quick >>>>> count of the number of lines, I see that there are some subjects that >>>>> have only 1 time point and some that have multiple time points, and that >>>>> the pathstats.byvoxel.txt files have different lengths between
Re: [Freesurfer] visualizing paths stats by voxel
Hey Anastasia, > Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki > : > > > Hi Janosch - There is a bug in how the output paths are saved when > longitudinal TRACULA is run with one time point only. I'm working on a fix. OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it! > In the meantime, you can try your analysis with the subjects that have > multiple time points and you won't be affected by this problem. I can see > that the subjects with a single time point are about 1/3 of your sample, and > so you may not want to drop them completely. Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis... > > Thank you for trying things that nobody else has tried and finding these bugs! Somebody has to be the first, eh? :) Thank you very much, Janosch > > More soon, > a.y > > On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: > >> Hey Anastasia, >> >> thanks for looking into this. >> >>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki >>> : >>> >>> >>> Hi Janosch - Looking at the stats files of your subjects, just by a quick >>> count of the number of lines, I see that there are some subjects that have >>> only 1 time point and some that have multiple time points, and that the >>> pathstats.byvoxel.txt files have different lengths between those two types >>> of subjects. >>> >>> I suspect that the strange average path that you get has to do with how >>> this mixing of subjects was done. Did you run the subjects with a single >>> time point through the longitudinal stream as well? >> >> Yes, I ran the longitudinal stream for all subjects, also for the ones with >> only one time point. >> >> Thanks, >> >> Janosch >> >>> >>> Best, >>> a.y >>> >>> On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: >>> >>>> Hi Anastasia, >>>> >>>> yes, I am. But it looks similar in the distributed version :( >>>> >>>> Thanks, >>>> >>>> Janosch >>>> >>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki >>>>> : >>>>> >>>>> >>>>> Hi Janosch - Are you by any chance using the dev version of freeview? >>>>> >>>>> a.y >>>>> >>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: >>>>> >>>>>> Hi Anastasia and list, >>>>>> >>>>>> I'm trying to do analyses along the tract with the path_stats_byvoxel >>>>>> files. >>>>>> >>>>>> When I am visualizing the points using the waypoint functionality of >>>>>> Freeview, it looks a little strange, i.e., the points are not equally >>>>>> spaces on the tract, but clumped together at some parts and spread out >>>>>> on others, see: >>>>>> >>>>>> >>>>>> >>>>>> this looks different to your slides: >>>>>> >>>>>> >>>>>> >>>>>> Also, the most posterior points seem to be strangely located (in the >>>>>> other hemisphere). What could be the reason for this strange behavior? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Janosch >>>>> >>>>> >>>>> 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
Re: [Freesurfer] visualizing paths stats by voxel
Hey Anastasia, thanks for looking into this. > Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki > : > > > Hi Janosch - Looking at the stats files of your subjects, just by a quick > count of the number of lines, I see that there are some subjects that have > only 1 time point and some that have multiple time points, and that the > pathstats.byvoxel.txt files have different lengths between those two types of > subjects. > > I suspect that the strange average path that you get has to do with how this > mixing of subjects was done. Did you run the subjects with a single time > point through the longitudinal stream as well? Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. Thanks, Janosch > > Best, > a.y > > On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: > >> Hi Anastasia, >> >> yes, I am. But it looks similar in the distributed version :( >> >> Thanks, >> >> Janosch >> >>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki >>> : >>> >>> >>> Hi Janosch - Are you by any chance using the dev version of freeview? >>> >>> a.y >>> >>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: >>> >>>> Hi Anastasia and list, >>>> >>>> I'm trying to do analyses along the tract with the path_stats_byvoxel >>>> files. >>>> >>>> When I am visualizing the points using the waypoint functionality of >>>> Freeview, it looks a little strange, i.e., the points are not equally >>>> spaces on the tract, but clumped together at some parts and spread out on >>>> others, see: >>>> >>>> >>>> >>>> this looks different to your slides: >>>> >>>> >>>> >>>> Also, the most posterior points seem to be strangely located (in the other >>>> hemisphere). What could be the reason for this strange behavior? >>>> >>>> Thanks, >>>> >>>> Janosch >>> >>> >>> 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
Re: [Freesurfer] visualizing paths stats by voxel
Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch > Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki > : > > > Hi Janosch - Are you by any chance using the dev version of freeview? > > a.y > > On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: > >> Hi Anastasia and list, >> >> I'm trying to do analyses along the tract with the path_stats_byvoxel files. >> >> When I am visualizing the points using the waypoint functionality of >> Freeview, it looks a little strange, i.e., the points are not equally spaces >> on the tract, but clumped together at some parts and spread out on others, >> see: >> >> >> >> this looks different to your slides: >> >> >> >> Also, the most posterior points seem to be strangely located (in the other >> hemisphere). What could be the reason for this strange behavior? >> >> Thanks, >> >> Janosch > > > 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
Re: [Freesurfer] Cluster correction in restricted space --> clusters outside of boundaries
Hi Doug, thanks for your answer. My commands are: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/labelname \ --base mc-z \ --surface fsaverage lh \ --nreps 1 \ --label /path/to/label/lh.labelname.label mri_glmfit --C /path/to/contrast/contrast.mtx \ --fsgd /path/to/fsgd/fsgd_file.fsgd dods \ --glmdir glm_dir \ --y /path/to/data/concat_lh_fsaverage_smooth15.mgz \ --surf fsaverage lh white mri_glmfit-sim --cache 2.00 neg \ --cache-label labelname \ --cwpvalthresh 0.05 \ --glmdir /path/to/glm_dir/glm_dir \ --overwrite \ --2spaces (this is for a cross-sectional case. In a longitudinal, I would use the glm_dir from a pseudo analysis and replace sig.mgh with the one from the matlab lme analysis as you have explained to me in my last thread) --- Because I run those commands embedded into a NiPype workflow, I had to modify mri_glmfit-sim a little: 1) because (I don't know why) the data file in the glmfit log file was not the correct one, mri_glmfit-sim was failing. --> So I changed the script so that it takes an --y argument (as mri_glmfit) to explicitly define the data file 2) because, when I only handed the glm_dir from the preceeding mri_glmfit step, different calls to mri_glmfit-sim (e.g., different --cache-label s) were all written into the same directory and overwriting each other. --> So I changed the script to copy the directory specified with --glmdir to the current folder and carry out all further operations on it Here a link to my modified mri_glmfit-sim version (https://dl.dropboxusercontent.com/u/255214/mri_glmfit-sim_nipype), I hope that these changes should not be responsible for the clustering I am experiencing?! Thanks a lot, Janosch > Can you send your mri_glmfit, mri_glmfit-sim, and mri_mcsim command lines? > > On 03/20/2015 02:24 PM, Janosch Linkersdörfer wrote: >> Hi all, >> >> I have a question/problem related to restricting monte carlo cluster >> correction to a reduced search space. >> >> I have: >> >> 1) created a label including the labels of regions I am interested in >> 2) used mri_mcsim with the --label flag and the label created in 1) to >> create >> cached monte carlo simulations for the search space >> 3) used mri_glmfit-sim with the --cache-label flag and the sim created in 2) >> >> The result is: >> >> - I definitively get more significant clusters than when I use the cortex >> label (so there must have been a reduction in search space/no. of vertices), >> but >> - some of these clusters lie only partly inside the regions included in the >> label >> - some lie even completely outside of the label >> >> I thought that I should get only clusters within the borders of the label so >> that vertices not in the label would not be considered. >> >> Thanks for your help, >> >> Janosch ___ 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] Cluster correction in restricted space --> clusters outside of boundaries
Hi all, I have a question/problem related to restricting monte carlo cluster correction to a reduced search space. I have: 1) created a label including the labels of regions I am interested in 2) used mri_mcsim with the --label flag and the label created in 1) to create cached monte carlo simulations for the search space 3) used mri_glmfit-sim with the --cache-label flag and the sim created in 2) The result is: - I definitively get more significant clusters than when I use the cortex label (so there must have been a reduction in search space/no. of vertices), but - some of these clusters lie only partly inside the regions included in the label - some lie even completely outside of the label I thought that I should get only clusters within the borders of the label so that vertices not in the label would not be considered. Thanks for your help, Janosch ___ 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] use of info from cortical parcellation in TRACULA
Hi Anastasia and others, I am sorry if I just did a bad job, but I could not find information on how information from the cortical parcellation is used in the path tracking done by TRACULA, especially, which cortical labels are used as determinants (seed, waypoint) for which tracts. It would be great if you could point me in the right direction! Thanks a lot, Janosch ___ 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] Monte Carlo simulation - Longitudinal Pipeline
Am 03.03.2015 um 14:42 schrieb Douglas N Greve : > > Some of this Martin will have to comment on, but my comments below > > On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: >> Hey Doug, >> >> thanks again! That means, I would do something like: >> >> 1.) construct longitudinal qdec table >> - only use fsid, fsid-base, and years/age columns >> - substract the average age of the one-time point subjects from years/age >> value for every subject at every time point >> >> 2.) run long_mris_slopes >> - use the --do-avg flag? > Yes, I think so >> >> 3.) concatenate the output files from 2) and the maps from the one-time >> point subjects with mris_preproc >> - use --is flag to select maps by specifying full path > What command are you talking about to do the concatenation? mris_preproc, I thought. Thanks for your help, Janosch > Otherwise sounds right. Make sure you use the average of the time points from > long_mris_slopes and not the slope. >> >> 4.) run mri_glmfit >> - use --osgm flag for one-sample group mean > Yes >> >> 5.) replace sig.mgz file with the one from LME analysis and run >> mri_glmfit-sim > Yes >> >> Is that correct? (especially, is using --do-avg what you meant by taking the >> offset) >> >> Thanks, >> >> Janosch >> >> >> Am 03.03.2015 um 08:32 schrieb Douglas N Greve : >> >>> I don't know, esp since it is an approximation to begin with. An >>> alternative is to take the offsets from your multi-time-point subjects and >>> the single maps from your subjects with one time point and run that through >>> the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, >>> then you should subtract the mean age of the one time-point subjects from >>> the age of the multi-time point subjects before the 1st stage of analysis. >>> >>> doug >>> >>> >>> On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: >>>> Hi Doug, >>>> >>>> thank you very much for your answer! >>>> >>>> Am 02.03.2015 um 11:30 schrieb Douglas N Greve : >>>> >>>>> You would do the long analysis using a random effects analysis. >>>> OK, so basically do 2-stage modeling >>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), >>>> right? >>>> >>>>> For each subject you can get a slope (this won't work if the subject only >>>>> has 1 time point), then concatenate the slopes into a file and run >>>>> mri_glmfit, then follow the procedures from the archive email you >>>>> reference. >>>> One quarter of my subjects only has one measurement time point. Can I >>>> still use this method (which would only consider the 3/4 of the subjects) >>>> to correct clusters found in the whole group? Or would it only be valid >>>> for correcting clusters from an LME model for the reduced group? >>>> >>>> Thanks, >>>> >>>> Janosch >>>> >>>>> doug >>>>> >>>>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: >>>>>> Hi Doug and others, >>>>>> >>>>>> I would like apply (Monte Carlo simulation) cluster correction (as >>>>>> opposed to the implemented vertex-wise FDR correction) on the results >>>>>> from a longitudinal study I analyzed using the LME toolbox. The design >>>>>> is unbalanced (different number of time points, from 1 to 4, per >>>>>> subject). >>>>>> >>>>>> In this thread >>>>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) >>>>>> you, Doug, suggested, if I understand correctly: >>>>>> >>>>>> - concatenating the images using `mris_preproc --paired-diff` >>>>>> - smooth with the same kernel size as used in the lme analysis >>>>>> - running `mri_glmfit` on them with an fsgd file that uses the same >>>>>> covariates and the same contrast (excluding the interaction term with >>>>>> time) as used in the lme analysis >>>>>> - overwriting sig.mgh with the one from the lme analysis >>>>>> - running `mri_glmfit-sim --cache` >>>>>> >>>>>> How would I extend this to my case where I don't ha
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes - use the --do-avg flag? 3.) concatenate the output files from 2) and the maps from the one-time point subjects with mris_preproc - use --is flag to select maps by specifying full path 4.) run mri_glmfit - use --osgm flag for one-sample group mean 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Is that correct? (especially, is using --do-avg what you meant by taking the offset) Thanks, Janosch Am 03.03.2015 um 08:32 schrieb Douglas N Greve : > > I don't know, esp since it is an approximation to begin with. An alternative > is to take the offsets from your multi-time-point subjects and the single > maps from your subjects with one time point and run that through the > one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you > should subtract the mean age of the one time-point subjects from the age of > the multi-time point subjects before the 1st stage of analysis. > > doug > > > On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: >> Hi Doug, >> >> thank you very much for your answer! >> >> Am 02.03.2015 um 11:30 schrieb Douglas N Greve : >> >>> You would do the long analysis using a random effects analysis. >> OK, so basically do 2-stage modeling >> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? >> >>> For each subject you can get a slope (this won't work if the subject only >>> has 1 time point), then concatenate the slopes into a file and run >>> mri_glmfit, then follow the procedures from the archive email you reference. >> One quarter of my subjects only has one measurement time point. Can I still >> use this method (which would only consider the 3/4 of the subjects) to >> correct clusters found in the whole group? Or would it only be valid for >> correcting clusters from an LME model for the reduced group? >> >> Thanks, >> >> Janosch >> >>> doug >>> >>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: >>>> Hi Doug and others, >>>> >>>> I would like apply (Monte Carlo simulation) cluster correction (as opposed >>>> to the implemented vertex-wise FDR correction) on the results from a >>>> longitudinal study I analyzed using the LME toolbox. The design is >>>> unbalanced (different number of time points, from 1 to 4, per subject). >>>> >>>> In this thread >>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) >>>> you, Doug, suggested, if I understand correctly: >>>> >>>> - concatenating the images using `mris_preproc --paired-diff` >>>> - smooth with the same kernel size as used in the lme analysis >>>> - running `mri_glmfit` on them with an fsgd file that uses the same >>>> covariates and the same contrast (excluding the interaction term with >>>> time) as used in the lme analysis >>>> - overwriting sig.mgh with the one from the lme analysis >>>> - running `mri_glmfit-sim --cache` >>>> >>>> How would I extend this to my case where I don't have pairwise images, but >>>> 1 image for some participants, for others up to 4? >>>> >>>> Thanks a lot, >>>> >>>> Janosch >>>> >>>> >>>> >>>> >>> -- >>> 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/ >>> >>> >>> >>> 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. >>> >> >> > > -- > 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] Monte Carlo simulation - Longitudinal Pipeline
Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve : > > You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? > For each subject you can get a slope (this won't work if the subject only has > 1 time point), then concatenate the slopes into a file and run mri_glmfit, > then follow the procedures from the archive email you reference. One quarter of my subjects only has one measurement time point. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch > doug > > On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: >> Hi Doug and others, >> >> I would like apply (Monte Carlo simulation) cluster correction (as opposed >> to the implemented vertex-wise FDR correction) on the results from a >> longitudinal study I analyzed using the LME toolbox. The design is >> unbalanced (different number of time points, from 1 to 4, per subject). >> >> In this thread >> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) >> you, Doug, suggested, if I understand correctly: >> >> - concatenating the images using `mris_preproc --paired-diff` >> - smooth with the same kernel size as used in the lme analysis >> - running `mri_glmfit` on them with an fsgd file that uses the same >> covariates and the same contrast (excluding the interaction term with time) >> as used in the lme analysis >> - overwriting sig.mgh with the one from the lme analysis >> - running `mri_glmfit-sim --cache` >> >> How would I extend this to my case where I don't have pairwise images, but 1 >> image for some participants, for others up to 4? >> >> Thanks a lot, >> >> Janosch >> >> >> >> > > -- > 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/ > > > > 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
[Freesurfer] mri_surfcluster questions
Hi all, I experimented with the different flags for mri_surfcluster and have 2 issues that I don't understand, it would be great if somebody could enlighten me: 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would expect, i.e., only clusters with a minimum vertex-wise p-value > thmin are shown. When I use 'neg' or 'pos', I get clusters with a minimum value below thmin. Why is that? 2) The FDR correction seems to be very lenient. Using --fdr .05, for example, I get a thmin of 1.158247. That is probably not correct, right? The command I use looks somewhat like: mri_surfcluster --sd /my/subj/dir --in sig.mgh --subject fsa verage(_DKT) --hemi lh --annot aparcDKT40 --sum summary.txt --clabel /path/to/label/lh.cortex.label [--fdr .05 | --thmin 3] --thsign [pos | neg | abs] Thanks, Janosch ___ 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] Monte Carlo simulation - Longitudinal Pipeline
Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per subject). In this thread (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) you, Doug, suggested, if I understand correctly: - concatenating the images using `mris_preproc --paired-diff` - smooth with the same kernel size as used in the lme analysis - running `mri_glmfit` on them with an fsgd file that uses the same covariates and the same contrast (excluding the interaction term with time) as used in the lme analysis - overwriting sig.mgh with the one from the lme analysis - running `mri_glmfit-sim --cache` How would I extend this to my case where I don't have pairwise images, but 1 image for some participants, for others up to 4? Thanks a lot, Janosch ___ 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] use of RFT script for cluster correction of results from lme analysis
Hi Don, Jorge, and list, I would like to do cluster-size based family-wise error correction on the results of a longitudinal analysis done with the lme toolbox. As Jorge told me that if I don't use spatiotemporal models, the use of RFT should be valid, I want to use the script posted on the list by Don (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg05717.html) and have some questions about the parameters to use: - when I want to correct for all vertices in the ?h.cortex.label, is it correct to take 'nvert' and 'surface area' as output by the command ```mris_info fsaverage/surf/?h.white``` - what command would I use to get these parameters for a smaller label (that merges only parcellations important for the subject of my study)? - for 'fwhm', do I just take the smoothing kernel width I used when preparing the data for group analysis? - how do I determine 'df' as they vary over the different vertices?. Would I just take the average or is there a smarter way? BTW, from experimenting with wildly different dfs (e.g., 10 vs 1000) dfs it seems that they result only in very litte differences in the FWE corrected cluster size output by the script. Is that correct? Thank you very much for your help! Janosch ___ 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] Rerun Tracula adding CVS registration
Great, thanks! Am 09.02.2015 um 13:10 schrieb Anastasia Yendiki : > > Hi Janosch - Yes, it's possible. In your config file use: > set doregmni = 0 > set doregcvs = 1 > > You do not need to rerun any of the preprocessing steps before the > inter-subject registration, so skip those when you run "trac-all -prep" to > save time. > > Hope this helps, > a.y > > On Mon, 9 Feb 2015, Janosch Linkersdörfer wrote: > >> Hey Anastasia (and list), >> >> I decided to go with affine registration to MNI when I processed my >> longitudinal dataset with Tracula, because I didn't realize that one has the >> option to do both MNI and CVS registration in parallel. >> >> Is there a way to rerun Tracula with the CVS option without having to rerun >> also with the MNI option? >> >> Thanks, >> >> Janosch >> >> >> > > > 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
[Freesurfer] Rerun Tracula adding CVS registration
Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't realize that one has the option to do both MNI and CVS registration in parallel. Is there a way to rerun Tracula with the CVS option without having to rerun also with the MNI option? Thanks, Janosch ___ 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] bvallist option in dmrirc file?
Hi Anastasia, Am 15.01.2015 um 16:14 schrieb Anastasia Yendiki : > > Sorry, I misunderstood. You have different numbers of directions not only > between subjects, but also between time points of the same subject? Yes, sadly. There a children who did good on some measurement time points and not so good on others... > I wouldn't recommend that. If your scans differ between time points, it'll be > impossible to tell whether within-subject changes that you find are due to > changes in the acquisition or actual changes in the brain. > Yes, it's at least questionable. So, would you also not implement the future option to exclude volumes for longitudinal tracula? BTW: - can I use the lme toolbox to do longitudinal statistics on the tracts identified by tracula or do I need the same number of dti scans for every subject? - If so, does it also work for statistics along the trajectory of a tract? Thanks a lot, Janosch > On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: > >> Hi Anastasia, >> >> I am already preparing separate dmrirc files for different subjects (but >> including all time points for a specific subject) because that way I can run >> them in parallel on different cores. >> >> I thought it was important to have all time points of a subject in one >> dmrirc file. If I understand you correctly, it's OK to have them in separate >> ones? Is the only thing that's needed to indicate longitudinal processing >> the "baselist" variable? >> >> If so, it would be great because I could run even more processes in parallel >> :) >> >> Thanks, >> >> Janosch >> >> Am 15.01.2015 um 15:51 schrieb Anastasia Yendiki >> : >> >>> >>> Hi Janosch - This makes sense. I do want to incorporate support for the >>> case where volumes are discarded for quality reasons in the next version, >>> but it's not possible in the current version unfortunately. You'll have to >>> generate separate config files for each case. Sorry for the hassle! >>> >>> a.y >>> >>> On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: >>> >>>> Hi Anastasia, >>>> >>>> in principle, all subjects were scanned with the same b-values (and bvecs >>>> for that matter). But as it is a pediatric sample, some of them don't have >>>> all volumes (67), because scans had to be aborted. We used a sequence that >>>> distributes the directions in a way that the data from aborted scans >>>> should still be processable. >>>> >>>> So, what I was trying to do was shorten the bvals (and bvecs) files to the >>>> length of the respective run (e.g., if it only has 54 volumes, the bvals >>>> and bvecs files are shortened to 54 lines) and include them on a per >>>> subject basis... >>>> >>>> Thanks, >>>> >>>> Janosch >>>> >>>>> Hi Janosch - Yes, it assumes that all subjects in your study where >>>>> scanned with the same b-values. What is your situation? >>>>> a.y >>>>> >>>>> On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: >>>>> >>>>> >>>>> Hi, >>>>> >>>>> I am trying to process diffusion data with the longitudinal TRACULA >>>>> stream. I >>>>> want to specify different bvecs and bvals files per scan in the dmrirc >>>>> file. >>>>> >>>>> For bvecs this is possible using >>>>> >>>>> bveclist = ... >>>>> >>>>> I tried to use >>>>> >>>>> bvallist = ... >>>>> >>>>> but apparently this does not seem to work because trac-all complains that >>>>> no >>>>> b-value file has been specified. >>>>> >>>>> Can only one bvalfile be specified for all scans? >>>>> >>>>> Thanks, >>>>> >>>>> Janosch >>>> >>>> >>>> >>> >>> >>> 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
Re: [Freesurfer] bvallist option in dmrirc file?
Hi Anastasia, I am already preparing separate dmrirc files for different subjects (but including all time points for a specific subject) because that way I can run them in parallel on different cores. I thought it was important to have all time points of a subject in one dmrirc file. If I understand you correctly, it's OK to have them in separate ones? Is the only thing that's needed to indicate longitudinal processing the "baselist" variable? If so, it would be great because I could run even more processes in parallel :) Thanks, Janosch Am 15.01.2015 um 15:51 schrieb Anastasia Yendiki : > > Hi Janosch - This makes sense. I do want to incorporate support for the case > where volumes are discarded for quality reasons in the next version, but it's > not possible in the current version unfortunately. You'll have to generate > separate config files for each case. Sorry for the hassle! > > a.y > > On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: > >> Hi Anastasia, >> >> in principle, all subjects were scanned with the same b-values (and bvecs >> for that matter). But as it is a pediatric sample, some of them don't have >> all volumes (67), because scans had to be aborted. We used a sequence that >> distributes the directions in a way that the data from aborted scans should >> still be processable. >> >> So, what I was trying to do was shorten the bvals (and bvecs) files to the >> length of the respective run (e.g., if it only has 54 volumes, the bvals and >> bvecs files are shortened to 54 lines) and include them on a per subject >> basis... >> >> Thanks, >> >> Janosch >> >>> Hi Janosch - Yes, it assumes that all subjects in your study where scanned >>> with the same b-values. What is your situation? >>> a.y >>> >>> On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: >>> >>> >>> Hi, >>> >>> I am trying to process diffusion data with the longitudinal TRACULA stream. >>> I >>> want to specify different bvecs and bvals files per scan in the dmrirc file. >>> >>> For bvecs this is possible using >>> >>> bveclist = ... >>> >>> I tried to use >>> >>> bvallist = ... >>> >>> but apparently this does not seem to work because trac-all complains that no >>> b-value file has been specified. >>> >>> Can only one bvalfile be specified for all scans? >>> >>> Thanks, >>> >>> Janosch >> >> >> > > > 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
Re: [Freesurfer] bvallist option in dmrirc file?
Hi Anastasia, in principle, all subjects were scanned with the same b-values (and bvecs for that matter). But as it is a pediatric sample, some of them don't have all volumes (67), because scans had to be aborted. We used a sequence that distributes the directions in a way that the data from aborted scans should still be processable. So, what I was trying to do was shorten the bvals (and bvecs) files to the length of the respective run (e.g., if it only has 54 volumes, the bvals and bvecs files are shortened to 54 lines) and include them on a per subject basis... Thanks, Janosch > Hi Janosch - Yes, it assumes that all subjects in your study where scanned > with the same b-values. What is your situation? > a.y > > On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: > > > Hi, > > I am trying to process diffusion data with the longitudinal TRACULA stream. I > want to specify different bvecs and bvals files per scan in the dmrirc file. > > For bvecs this is possible using > > bveclist = ... > > I tried to use > > bvallist = ... > > but apparently this does not seem to work because trac-all complains that no > b-value file has been specified. > > Can only one bvalfile be specified for all scans? > > Thanks, > > Janosch ___ 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] bvallist option in dmrirc file?
Hi, I am trying to process diffusion data with the longitudinal TRACULA stream. I want to specify different bvecs and bvals files per scan in the dmrirc file. For bvecs this is possible using bveclist = ... I tried to use bvallist = ... but apparently this does not seem to work because trac-all complains that no b-value file has been specified. Can only one bvalfile be specified for all scans? Thanks, Janosch ___ 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] Restrict lme analysis results/FDR correction to ROIs from atlas labels
Hi Freesurfers, after running through the longitudinal stream and modeling with linear mixed effect models, I would like to restrict the analysis to only specific ROIs and run FDR correction for vertices included in them. - I think I can do this with mri_surfclusters with the --mask option, right? - How can I make a mask from labels of one of the 3 atlases (from fsaverage) that can be used in this step? Additional: - I don't see an annot file for the DKT atlas in fsaverage/label. To use labels from this atlas, what would I have to do first? Thank you very much, Janosch ___ 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] Digest mode for mailing list and responding to mails
Hi list, I recently switched to the digest mode for the mailing list. Since then, I don't receive answers to my mails as mails anymore, making it harder to respond to them (or any other mail on the list). Does anybody experience the same issues? How did you solve them? Thanks, Janosch ___ 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] Tracula mri_convert error
Hi experts,
I wanted to play with Tracula. Strangely, already the first preprocessing step,
i.e., conversion to .nii.gz, fails.
Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms
("This looks like an MGH DTI volume"). Could this be the reason why it fails?
Thanks,
Janosch
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[Freesurfer] Download of latest Tracula version not possible
Hi all, I am trying to download the latest version of Tracula from this site http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. This seems not to be possible at the moment. Are there server problems? Thanks, Janosch ___ 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] Changing subject names after processing
Great, I'll do that. Thank you very much! Am 26.10.2014 um 17:12 schrieb Martin Reuter : > One possible solution: > Rename the time point in cross, in the base txt file (directly under the base > directory, something with tps in it), in the base/mri/transforms/* files and > in the long directory names and long/mri/transform files. I think these are > all the places where subject names are stored, but no guarantee. > Best Martin > > > Sent via my smartphone, please excuse brevity. > > ---- Original message > From: Janosch Linkersdörfer > Date:10/26/2014 6:05 PM (GMT-05:00) > To: mreu...@nmr.mgh.harvard.edu > Cc: Freesurfer support list > Subject: Re: [Freesurfer] Changing subject names after processing > > Hi Martin and Doug, > > thanks for your answers! > > >>> theoretically it would be sufficient > to rename the longitudinal directories accordingly as the base should > not change at all, only some of the filenames -- not tested! > > Did I understand it correctly that if one has gone through the whole > longitudinal processing stream (including corrections etc.), could one not > remove the crosses and the base and just rename the longs to the new name as > any further processing/stats is carried out only with them? > > Thanks, > > Janosch > > > > 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
Re: [Freesurfer] Changing subject names after processing
Hi Martin and Doug, thanks for your answers! >>> theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole longitudinal processing stream (including corrections etc.), could one not remove the crosses and the base and just rename the longs to the new name as any further processing/stats is carried out only with them? Thanks, Janosch ___ 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] Changing subject names after processing
Hi all, I wonder whether I can rename subjects after processing has been done and do further processing or stats on them without running in any problems. >From reading >http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg26244.html, it >seems as if the name of the subject folder under which everything else resides >is the only marker and renaming it should be sufficient. But it seems the subject name is written in other places (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19285.html). Is this only a problem for de-identification or could it also cause other problems if the subject folder name and the name that is used elsewhere in the tree don't match. Are there special considerations regarding the longitudinal workflow? Thanks, Janosch ___ 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] watershed error again
Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log ). The image quality does not seem to be different... The error has been discussed on the list ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.html ), but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. --- Thanks for your help, Janosch ___ 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] Longitudinal troubleshooting
Hi Martin and all, I am about to process a large longitudinal dataset (normal development, no patients) and wanted to ask about the best (i.e., time efficient) strategy for troubleshooting. If I understand correctly from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits, it might be OK in my case (only little longitudinal changes expected) to only edit the base runs and transfer those edits to the long runs. So I thought of doing the following: - use the QA tools to export detailed snapshots of all base runs - check the snapshots for errors - use Freeview to add control points / edit white matter in brainmask.mgz of the base runs (while simultaneously checking whether those edits would make sense in brainmask.mgz of all long runs of the same subject) - rerun base - rerun longs Does that make sense? Thanks, Janosch ___ 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] watershed error
Hi all, recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log). The image quality does not seem to be different... The error has been discussed on the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.html), but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. Thanks for your help, Janosch ___ 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] Installing only Freeview
A stand-alone build would be great! Thanks Am 11.04.2014 um 16:59 schrieb Ruopeng Wang : > OK. I'll put in license checking. > > On 04/11/2014 10:57 AM, Bruce Fischl wrote: >> I think we need to distribute it with a license for NIH-accounting >> purposes. The license is free and trivial to get so it's not really >> much of a hardship >> On Fri, 11 Apr 2014, Ruopeng Wang wrote: >> >>> I have a stand-alone FreeView build for Mac that doesn't even need >>> license file to run. Can we distribute it? >>> >>> Ruopeng >>> >>> On 04/11/2014 10:53 AM, Bruce Fischl wrote: >>>> probably all you need is the freeview binary and the license file, >>>> but Ruopeng can confirm >>>> Bruce >>>> On Fri, 11 Apr 2014, Janosch Linkersdörfer wrote: >>>> >>>>> Hi all, >>>>> >>>>> is there a way, to install only freeview not the whole Freesurfer >>>>> package (on Mac OS X). Or, alternatively, can somebody please tell >>>>> me what I can safely remove after installing the whole package to >>>>> be able to still run Freeview, but save the maximum of hard disk >>>>> space? >>>>> >>>>> I do all processing on a remote computing server, but my VNC >>>>> connection does not allow to display freeview, so I use sshfs to >>>>> mount the server locally on my MacBook and use the local Freeview >>>>> to inspect or correct files. >>>>> >>>>> Thanks, >>>>> >>>>> Janosch >>>>> ___ >>>>> 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
[Freesurfer] Installing only Freeview
Hi all, is there a way, to install only freeview not the whole Freesurfer package (on Mac OS X). Or, alternatively, can somebody please tell me what I can safely remove after installing the whole package to be able to still run Freeview, but save the maximum of hard disk space? I do all processing on a remote computing server, but my VNC connection does not allow to display freeview, so I use sshfs to mount the server locally on my MacBook and use the local Freeview to inspect or correct files. Thanks, Janosch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?
Thanks, Anastasia! Am 01.04.2014 um 17:36 schrieb Anastasia Yendiki : > > Hi Janosch - The December 9th tracula update is just that, an update to the > tracula code without any changes to the rest of freesurfer. > > a.y > > On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: > >> Hi all, >> >> I am a little confused about what the latest Freesurfer version is. >> >> I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw >> in the Tracula update list that there is apparently a version from December >> 9, 2013. >> >> Could you please clear that up for me? >> >> Thanks, >> >> Janosch >> ___ >> 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
[Freesurfer] Freesurfer version after 5.3.0 from May 2013?
Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw in the Tracula update list that there is apparently a version from December 9, 2013. Could you please clear that up for me? Thanks, Janosch ___ 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] Troubleshooting - uncertainty about adding control points
Hi Bruce, thanks for your answer! Am 30.01.2014 um 14:40 schrieb Bruce Fischl : > Hi Janosch > > it's impossible to tell from a single slice whether those points should be > added or not. The white matter in your image is *very* dark in these regions, > do you know why? No, I don't know why, is that something to worry about? The screen shot is from a child participant, but it seems my images (includung the ones from adults) are darker than the ones provided in the tutorial overall. We used an optimized MDEFT sequence with the following settings Slices 176 Voxel size 1x1x1mm Orientation sagittal FoV 256x224 Matrix 224x256 TR 7.92 FA 16 TE 2.48 TI 910 PAT modeGrappa 2 Fat suppr fat sat Coil8ch. Head Bandwidth 195 Phase enc.dir A->P see Deichmann, R., Schwarzbauer, C., & Turner, R. (2004). Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T. NeuroImage, 21(2), 757–767. > To decide whether to add them or not you should check a couple of slices in > each direction (or look in multiple orientations) to make sure that the white > matter is actually dark and it's not partial volume effects. The approach I > would take is iterative - add a couple then rerun up to the first inflation > and see if things have been improved significantly. This is fast, maybe 5-10 > minutes, not sure. Thanks, I will try this approach. > You shouldn't need to add a ton. Even one control point in the middle of a > dark region can have a large effect. I still wonder which is the desired outcome state. Is it important that the white matter border follows *exactly* the one I perceive on every slice or is it OK when on some sclices it does not. Regarding the tutorial data: Can cp_after considered to be a completely corrected example subject or is only the one area corrected that the tutorial points to and the rest of the images would also have to be modified?! I see some areas in cp_before AND cp_after where I am not sure whether adding control points would be needed. It would help me if you could point me to one or two completely corrected and perfectly processed images so I could determine what level of accuracy is desirable. Sorry for all these questions, but I think modifying the images is a crucial point in the process that influences all further steps, and I just don't yet have a feeling for it... Thanks, Janosch > > cheers > Bruce > > > On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote: > >> Dear Freesurfers, >> >> I am just getting started using Freesurfer. I ran recon-all on my subjects >> for the first time and now would like to troubleshoot the output. >> >> I watched the tutorial lectures and worked through the troubleshooting >> tutorial. Nevertheless, I am still uncertain which things I will have to >> correct (especially as editing too much and/or not to the same degree >> between subjects might do more harm than good). >> >> Some errors are relatively obvious like the exclusion of white matter voxels >> from the white matter surface (see *1* on the screen shot of my own data) >> >> >> >> I am far more uncertain about adding control points. For example, I do not >> know whether I should add those at the location denoted with *2* in my own >> data. >> >> If so, there would be a lot of other, similar locations where I would add >> control points in my data. But this would also be true for the image used in >> the "Adding control points" tutorial. In the second screen shot, which >> displays this image, I have marked some locations where the white matter >> surface does not follow the one I would draw if I had to do it manually. >> >> >> >> Is one supposed to correct all those imprecisions by adding control points?! >> What are the criteria for adding vs. not adding control points? >> >> Thank you very much, >> >> Janosch >> >> >> > > > 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
Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis
Dear Martin and Bruce, thank you very much for your detailed answers! This helps a lot! Best, Janosch Am 15.01.2014 um 21:53 schrieb Martin Reuter : > Hi Janosch, > > there is no fixed naming convention for subjectids from our side, only > recommendations. If you like you can call the first time point of subject1 > 'mike' and the second time point of the same subject 'peter' , we don't care, > but it would be confusing. > > We recommend a convention where you have > > subjectid_tp1 > subjectid_tp2 > > or > subjectid01 > ... > or > subjectidA > subjectidB > > etc. > > that makes things easier, but is not necessary. > > For cross sectional processing you can place these wherever you want and > process a subject_tp at a time in a different location if you like. For > longitudinal processing you need to create a single directory where all of > these are symlinked (we only need read access). You can do this on a > per-subject-basis or for all subjects which is often simpler. The -base run > then creates additional directories that may look like > subjectid > or > subjectid_base > or > subjectid_template > (depending on how you name it). > > The -long runs finally create additional directories that look like > subjectid_tp1.base.subjectid > (or ...base.subjectid_tempalte again depending on how you named the base). > > If you want (for further postprocessing scripts) you can create a different > directory structure similar to what you did for the cross sectional runs and > symlinking the *.long.* into that structure, but any processing needs to be > done in the single directory that has all time points and base and long runs. > > Hope that helps, > Best, Martin > > > On 01/15/2014 01:40 PM, Bruce Fischl wrote: >> >> I'll leave this for Martin >> Bruce >> >> On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote: >> >>> Hi Bruce, >>> >>> thank you very much for your answer! >>> >>> Am 15.01.2014 um 14:33 schrieb Bruce Fischl : >>> >>>> Hi Janosch >>>> >>>> it will certainly make your life easier if you don't change the names. >>> >>> So the subject names are saved in other places/files than the folder name? >>> >>>> Symlinking is fine if you keep the same name, but particularly for the >>>> longitudinal runs the names have meaning and are stored in files like the >>>> tps one which stores the timepoints that went into the base. >>> >>> OK, so if I understand you correctly, the folder structure for the initial >>> processing does not matter as I can collect different subjects from >>> different places in one $SUBJECTS_DIR for doing (cross-sectional or >>> longitudinal) stats by either copying or symlinking their subject folders. >>> >>> But the name of the symlink has to be the same as the one used in the >>> initial processing, so I would have to include the time point in the >>> subject name even in the initial processing? >>> >>> BTW, does one have to use your naming scheme, i.e., "tp1SUBJECTID" or is >>> this flexible, e.g., "tp0_SUBJECTID", "SUBJECTID_tp1", "2011__SUBJECTID", >>> etc.? >>> >>> Thanks a lot, >>> >>> Janosch >>> >>> >>>> >>>> cheers >>>> Bruce >>>> On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote: >>>> >>>>> Hi, >>>>> >>>>> sorry if my question was to basic, but I would really appreciate if >>>>> somebody could give me some insight into whether the folder organization >>>>> and the subject name used in the first run of recon-all have to be stable >>>>> over all all following processing steps or if one can, e.g., change the >>>>> names of the subject folders and/or symlink them to another location >>>>> (with another name) and continue with further processing. >>>>> >>>>> Thanks, >>>>> >>>>> Janosch >>>>> >>>>> Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer >>>>> : >>>>> >>>>>> Hi all, >>>>>> >>>>>> I have 4 years of structural scans from children and 2 from adults. I >>>>>> would like to analyze the data both cross-sectionally and >>>>>>
Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis
Hi Bruce, thank you very much for your answer! Am 15.01.2014 um 14:33 schrieb Bruce Fischl : > Hi Janosch > > it will certainly make your life easier if you don't change the names. So the subject names are saved in other places/files than the folder name? > Symlinking is fine if you keep the same name, but particularly for the > longitudinal runs the names have meaning and are stored in files like the tps > one which stores the timepoints that went into the base. OK, so if I understand you correctly, the folder structure for the initial processing does not matter as I can collect different subjects from different places in one $SUBJECTS_DIR for doing (cross-sectional or longitudinal) stats by either copying or symlinking their subject folders. But the name of the symlink has to be the same as the one used in the initial processing, so I would have to include the time point in the subject name even in the initial processing? BTW, does one have to use your naming scheme, i.e., "tp1SUBJECTID" or is this flexible, e.g., "tp0_SUBJECTID", "SUBJECTID_tp1", "2011__SUBJECTID", etc.? Thanks a lot, Janosch > > cheers > Bruce > On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote: > >> Hi, >> >> sorry if my question was to basic, but I would really appreciate if somebody >> could give me some insight into whether the folder organization and the >> subject name used in the first run of recon-all have to be stable over all >> all following processing steps or if one can, e.g., change the names of the >> subject folders and/or symlink them to another location (with another name) >> and continue with further processing. >> >> Thanks, >> >> Janosch >> >> Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer >> : >> >>> Hi all, >>> >>> I have 4 years of structural scans from children and 2 from adults. I would >>> like to analyze the data both cross-sectionally and longitudinally. In the >>> recommendations for the longitudinal analysis, it says one should process >>> all images in one folder with the time point in the subjectID/subject >>> folder, e.g., >>> >>> .../data/tp1_subj001 >>> .../data/tp2_subj001 >>> .../data/tp3_subj001 >>> .../data/tp4_subj001 >>> .../data/tp1_subj002 >>> ... >>> >>> For the cross-sectional analyses, I would like to organize the analyses in >>> folders for subject age and year, e.g., >>> >>> .../data/children/tp1/subj001 >>> .../data/children/tp1/subj002 >>> .../data/children/tp2/subj001 >>> .../data/children/tp2/subj002 >>> ... >>> .../data/adults/tp1/adult_subj001 >>> .../data/adults/tp1/adult_subj002 >>> .../data/adults/tp2/adult_subj001 >>> .../data/adults/tp2/adult_subj001 >>> >>> Is it possible to organize the data this way and to symlink the individual >>> folders into another folder for the longitudinal analysis, i.e., >>> >>> .../longitudinal_analysis/tp1_subj001 -> .../data/children/tp1/subj001 >>> .../longitudinal_analysis/tp2_subj001 -> .../data/children/tp2/subj001 >>> ... >>> >>> Additionally, are there any considerations regarding renaming/moving >>> subject folders (as long as anything inside a subject folder remains >>> unchanged), i.e. are there any hard links or similar that would break >>> further processing? >>> >>> Thanks a lot! >>> >>> Janosch >> >> >> ___ >> 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
Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis
Hi, sorry if my question was to basic, but I would really appreciate if somebody could give me some insight into whether the folder organization and the subject name used in the first run of recon-all have to be stable over all all following processing steps or if one can, e.g., change the names of the subject folders and/or symlink them to another location (with another name) and continue with further processing. Thanks, Janosch Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer : > Hi all, > > I have 4 years of structural scans from children and 2 from adults. I would > like to analyze the data both cross-sectionally and longitudinally. In the > recommendations for the longitudinal analysis, it says one should process all > images in one folder with the time point in the subjectID/subject folder, > e.g., > > .../data/tp1_subj001 > .../data/tp2_subj001 > .../data/tp3_subj001 > .../data/tp4_subj001 > .../data/tp1_subj002 > ... > > For the cross-sectional analyses, I would like to organize the analyses in > folders for subject age and year, e.g., > > .../data/children/tp1/subj001 > .../data/children/tp1/subj002 > .../data/children/tp2/subj001 > .../data/children/tp2/subj002 > ... > .../data/adults/tp1/adult_subj001 > .../data/adults/tp1/adult_subj002 > .../data/adults/tp2/adult_subj001 > .../data/adults/tp2/adult_subj001 > > Is it possible to organize the data this way and to symlink the individual > folders into another folder for the longitudinal analysis, i.e., > > .../longitudinal_analysis/tp1_subj001 -> .../data/children/tp1/subj001 > .../longitudinal_analysis/tp2_subj001 -> .../data/children/tp2/subj001 > ... > > Additionally, are there any considerations regarding renaming/moving subject > folders (as long as anything inside a subject folder remains unchanged), i.e. > are there any hard links or similar that would break further processing? > > Thanks a lot! > > Janosch ___ 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] Folder organization cross-sectional/longitudinal analysis
Hi all, I have 4 years of structural scans from children and 2 from adults. I would like to analyze the data both cross-sectionally and longitudinally. In the recommendations for the longitudinal analysis, it says one should process all images in one folder with the time point in the subjectID/subject folder, e.g., .../data/tp1_subj001 .../data/tp2_subj001 .../data/tp3_subj001 .../data/tp4_subj001 .../data/tp1_subj002 ... For the cross-sectional analyses, I would like to organize the analyses in folders for subject age and year, e.g., .../data/children/tp1/subj001 .../data/children/tp1/subj002 .../data/children/tp2/subj001 .../data/children/tp2/subj002 ... .../data/adults/tp1/adult_subj001 .../data/adults/tp1/adult_subj002 .../data/adults/tp2/adult_subj001 .../data/adults/tp2/adult_subj001 Is it possible to organize the data this way and to symlink the individual folders into another folder for the longitudinal analysis, i.e., .../longitudinal_analysis/tp1_subj001 -> .../data/children/tp1/subj001 .../longitudinal_analysis/tp2_subj001 -> .../data/children/tp2/subj001 ... Additionally, are there any considerations regarding renaming/moving subject folders (as long as anything inside a subject folder remains unchanged), i.e. are there any hard links or similar that would break further processing? Thanks a lot! Janosch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer course troubleshooting presentation slides
Hi, thank you very much for providing the lectures of the last Freesurfer course as videos! I am just watching them, and it seem that the .ppt file provided for the troubleshooting lecture does not match the slides used in the video. It would be great if you could provide the slides used in the video! Thanks, J ___ 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] mri_convert introduces flip
Hi experts, I´m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... - INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file - TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch ___ 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.
