Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011
Hi Annie, I have previously extracted individual regions from the 7 and 17 networks. You can download them here (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0). Please see the README in the folder for more explanations. There should be a precuneus DMN region. The 17 networks consist of 114 regions that have been previously published: 1) Krienen et al., Reconfigurable state-dependent functional coupling modes cluster around a core functional architecture. Philosophical Transactions of the Royal Society B, 369:20130526, 2014 2) Yeo et al., Functional connectivity during rested wakefulness predicts vulnerability to sleep deprivation. Neuroimage 111:147-158, 2015 Hope this helps. Cheers, Thomas On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 wrote: > Hello Dr. Yeo, > > Thank you for your previous help and reply. We've worked out the way to > switch the resolution of parcellation and successfully extracted the > anatomical information using your mask derived from iFC work. > > However, we came across a new problem to apply the cortical mask and need > your kind help again. We aim to conduct a seed-based analysis to investigate > structural covariance based on the network defined by iFC, and find your > work of cortical parcellation conceptually perfectly suit our research > question. Based on the current approach, however, it seemed that we could > only extract the anatomical information from the whole well-defined network, > but not the specific hub within the network (e.g., the anatomical > information of the precuneus from the DMN). We wonder if you have any > suggestion to resolve our problem, ie, to be specific, is there any way to > only extract the discrete hub information rather than the whole network? > > We really appreciate your generous help. Thank you very much. > > p.s. This email would also forward to my senior colleague, Dr. Hsiang-Yuan > Lin, who is a child and adolescent psychiatrist doing imaging research in > Taiwan. > > > 2015-05-13 19:15 GMT+08:00 陳昱潔 : >> >> Hi Professor Yeo : >> >> Thank you for helping us so much! >> After mris_anatomical_stat I tried aparcstats2table to extract the table. >> But I failed with generating the table. >> >> >> Best wishes, >> Annie >> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo : >> >>> Hi Annie, >>> >>> I assume this means 5202 is your subject ID? Maybe you should check if >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot >>> exist? >>> >>> If so, you can run mris_anatomical_stats to generate statistics for >>> the parcellation. >>> >>> Cheers, >>> Thomas >>> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 wrote: >>> > Hi Professor Yeo : >>> > After I rechecked the directory and run again mri_surf2surf >>> > I got the result: >>> > "Saving target data >>> > Converting to target annot >>> > Saving to target annot >>> > >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot" >>> > The file of 5202/label didn't come out with >>> > lh.Yeo2011_7Networks_N1000.annot >>> > But it seems succeed, right? >>> > How can I get the stat of this parcellation ? >>> > >>> > Thank you very much! >>> > >>> > Best wishes, >>> > Annie >>> > >>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo : >>> > >>> >> Hi Annie, >>> >> >>> >> mri_surf2surf is complaining that it cannot write out the annotation. >>> >> >>> >> Just to clarify, is your subject called test_run_allindex? In other >>> >> words, is the variable s equal to test_run_allindex? >>> >> >>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? If >>> >> not, then you first need to create the directory first, and then >>> >> mri_surf2surf can write the resulting annotation file into the >>> >> directory. >>> >> >>> >> Cheers, >>> >> Thomas >>> >> >>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 wrote: >>> >> > Hi Professor Yeo : >>> >> > >>> >> >We tried the code >>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh >>> >> >>> --sval-annot >>> >> >>> >>> >> >>> >>> >> >>> >>> >> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot >>> >> >>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot >>> >> > However there came an error of "could not write annot file >>> >> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot >>> >> > No such file or directory" >>> >> > And we checked our individual subject's label there isn't >>> >> > lh.Yeo2011_7Networks_N1000.annot >>> >> > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into >>> >> > our >>> >> > subjects/label first? >>> >> > What can we do ? >>> >> > Thank you very much! >>> >> > >>> >> > Best wishes, >>> >> > Annie >>> >> > >>> >> > >>> >> > 2015-05-05 8:36 GMT-04:00 Thomas Yeo : >>> >> > >>> >> >> Hi Annie, >>> >> >> >>> >> >> Please cc the freesurfer list when you reply because there might be >>> >> >> other people more qualified to answer your question. >>> >> >> >>> >> >> Based on what you are say
[Freesurfer] Freeview mountain lion
Hi there,I recently tried to update the Freeview version so I can have the recon edit button. I managed to copy the file over but now I get the following error:dyld: Library not loaded: @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Reason: image not foundTrace/BPT trapWhen I double click on the Freeveiw app I get a more detailed error:Process: Freeview [10010]Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/FreeviewIdentifier: FreeviewVersion: ???Code Type: X86-64 (Native)Parent Process: tcsh [10008]User ID: 501Date/Time: 2015-05-14 08:33:50.177 -0400OS Version: Mac OS X 10.8.5 (12F2518)Report Version: 10Interval Since Last Report: 858 secCrashes Since Last Report: 2Per-App Crashes Since Last Report: 2Anonymous UUID: 83D92F1C-F624-48C3-3831-9BD909D04175Crashed Thread: 0Exception Type: EXC_BREAKPOINT (SIGTRAP)Exception Codes: 0x0002, 0xApplication Specific Information:dyld: launch, loading dependent librariesDyld Error Message: Library not loaded: @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Reason: image not foundBinary Images: 0x1046ba000 - 0x105d9efe7 +com.yourcompany.Freeview (???) /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview 0x106c8a000 - 0x106c94ff7 +libgomp.1.dylib (2) <33BB1457-AC5A-343C-B6FA-F70EEC21BF69> /Users/USER/*/libgomp.1.dylib 0x106ca6000 - 0x106efdfe7 +QtScript (4.7.4) <22C41B2A-3C52-B7E9-37A8-EF71E48EE9FB> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtScript.framework/Versions/4/QtScript 0x106f56000 - 0x1071deff7 +QtCore (4.7.4) <9EB52EC3-3C0F-0A45-1CE6-227EB7069767> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore 0x7fff642ba000 - 0x7fff642ee94f dyld (210.2.3) <8958FE97-5830-3928-BC38-23136E7D3783> /usr/lib/dyld 0x7fff8e6be000 - 0x7fff8e6befff com.apple.Cocoa (6.7 - 19) <1F77945C-F37A-3171-B22E-F7AB0FCBB4D4> /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 0x7fff8eb63000 - 0x7fff8ebd1fff com.apple.framework.IOKit (2.0.1 - 755.42.2) <18E64CC5-2671-3C47-B2C6-0EEEDF899461> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit 0x7fff8f5e1000 - 0x7fff8f5e1fff com.apple.Accelerate (1.8 - Accelerate 1.8) <878A6E7E-CB34-380F-8212-47FBF12C7C96> /System/Library/Frameworks/Accelerate.framework/Versions/A/AccelerateModel: MacBookPro9,2, BootROM MBP91.00D3.B09, 2 processors, Intel Core i7, 2.9 GHz, 8 GB, SMC 2.2f44Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, 512 MBMemory Module: BANK 0/DIMM0, 4 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3431554638424455352D474E2D4620Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3431554638424455352D474E2D4620AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xF5), Broadcom BCM43xx 1.0 (5.106.98.100.17)Bluetooth: Version 4.1.7f5 15113, 3 service, 21 devices, 3 incoming serial portsNetwork Service: Ethernet, Ethernet, en0Serial ATA Device: APPLE HDD HTS541010A9E662, 1 TBSerial ATA Device: MATSHITADVD-R UJ-8A8USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1a10 / 2USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8509, 0x1a11 / 3USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1d10 / 2USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0x1d18 / 3USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0253, 0x1d183000 / 6USB Device: IR Receiver, apple_vendor_id, 0x8242, 0x1d182000 / 5USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1d181000 / 4USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821d, 0x1d181300 / 9I would really like to be able to use the recon edit button. Any suggestions regarding how this can be fixed?Thanks,Isabelle ___ 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: Problem with Freesurfer 5.3
Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i /9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i /9-2-1.dcm recon-all -s Pat2 \ -i /9-2-1.dcm and so on (2) recon-all -s -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Could that be an bug in the program? Once again! Thank you for your help! Best regards; Cecilio. 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez : Thank you so much for your quick and helpful response!Best regards, Cecilio. 2015-04-26 20:27 GMT+08:00 Bruce Fischl
[Freesurfer] Help FreeSurfer
Dear FreeSurfer Users, I have tried to download FreeSurfer but I am not sure I’ve done it correctly. Could you send me a guide to download it properly? Inside freesurfer there is only “Freeview” as a program. Is that correct? I notice that there is a folder “matlab”, isn’t there a description of the functions inside it? Thanks and best regards. M.F. ___ 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] Freeview mountain lion
Hello Isabelle, Freeview has been undergoing many changes and you simply got unlucky and downloaded an unstable version of the program. I will be posting an updated version within the day and I will email you directly when it becomes available. -Zeke > Hi > there,I recently tried to update the Freeview version > so I can have the recon edit button. I managed to copy the file over but > now I get the following error:dyld: Library > not loaded: > @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools > Referenced from: > /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview > Reason: image not foundTrace/BPT > trapWhen I double click on the Freeveiw > app I get a more detailed error:Process: > Freeview [10010]Path: > > /Applications/freesurfer/Freeview.app/Contents/MacOS/FreeviewIdentifier: > FreeviewVersion: > ???Code Type: X86-64 > (Native)Parent Process: tcsh [10008]User ID: > 501Date/Time: > 2015-05-14 08:33:50.177 -0400OS Version: > Mac OS X 10.8.5 (12F2518)Report Version: > 10Interval Since Last Report: > 858 secCrashes Since Last Report: > 2Per-App Crashes Since Last > Report: 2Anonymous UUID: > > 83D92F1C-F624-48C3-3831-9BD909D04175Crashed > Thread: 0Exception Type: > EXC_BREAKPOINT (SIGTRAP)Exception Codes: > 0x0002, > 0xApplication Specific > Information:dyld: launch, loading dependent > librariesDyld Error Message: > Library not loaded: > @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools > Referenced from: > /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview > Reason: image not foundBinary > Images: 0x1046ba000 - > 0x105d9efe7 +com.yourcompany.Freeview (???) >> /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview > 0x106c8a000 - 0x106c94ff7 > +libgomp.1.dylib (2) <33BB1457-AC5A-343C-B6FA-F70EEC21BF69> > /Users/USER/*/libgomp.1.dylib > 0x106ca6000 - 0x106efdfe7 +QtScript > (4.7.4) <22C41B2A-3C52-B7E9-37A8-EF71E48EE9FB> > /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtScript.framework/Versions/4/QtScript > 0x106f56000 - 0x1071deff7 > +QtCore (4.7.4) <9EB52EC3-3C0F-0A45-1CE6-227EB7069767> > /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore > 0x7fff642ba000 - 0x7fff642ee94f dyld (210.2.3) > <8958FE97-5830-3928-BC38-23136E7D3783> > /usr/lib/dyld 0x7fff8e6be000 - > 0x7fff8e6befff com.apple.Cocoa (6.7 - 19) > <1F77945C-F37A-3171-B22E-F7AB0FCBB4D4> > /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa > 0x7fff8eb63000 - 0x7fff8ebd1fff > com.apple.framework.IOKit (2.0.1 - 755.42.2) > <18E64CC5-2671-3C47-B2C6-0EEEDF899461> > /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit > 0x7fff8f5e1000 - 0x7fff8f5e1fff > com.apple.Accelerate (1.8 - Accelerate 1.8) > <878A6E7E-CB34-380F-8212-47FBF12C7C96> > /System/Library/Frameworks/Accelerate.framework/Versions/A/AccelerateModel: > MacBookPro9,2, BootROM MBP91.00D3.B09, 2 processors, Intel Core i7, 2.9 > GHz, 8 GB, SMC 2.2f44Graphics: Intel HD Graphics 4000, Intel HD > Graphics 4000, Built-In, 512 MBMemory Module: BANK 0/DIMM0, 4 > GB, DDR3, 1600 MHz, 0x02FE, > 0x45424A3431554638424455352D474E2D4620Memory Module: BANK > 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x02FE, > 0x45424A3431554638424455352D474E2D4620AirPort: > spairport_wireless_card_type_airport_extreme (0x14E4, 0xF5), Broadcom > BCM43xx 1.0 (5.106.98.100.17)Bluetooth: Version 4.1.7f5 15113, > 3 service, 21 devices, 3 incoming serial portsNetwork Service: > Ethernet, Ethernet, en0Serial ATA Device: APPLE HDD > HTS541010A9E662, 1 TBSerial ATA Device: MATSHITADVD-R > UJ-8A8USB Device: hub_device, 0x8087 (Intel Corporation), > 0x0024, 0x1a10 / 2USB Device: FaceTime HD Camera > (Built-in), apple_vendor_id, 0x8509, 0x1a11 / 3USB Device: > hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1d10 / > 2USB Device: hub_device, 0x0424 (SMSC), 0x2513, > 0x1d18 / 3USB Device: Apple Internal Keyboard / Trackpad, > apple_vendor_id, 0x0253, 0x1d183000 / 6USB Device: IR Receiver, > apple_vendor_id, 0x8242, 0x1d182000 / 5USB Device: BRCM20702 > Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1d181000 / 4USB > Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821d, 0x1d181300 > / 9I would really like to be able to use > the recon edit button. Any suggestions regarding how this can be > fixed?Thanks,Isabelle apple-content-edited="true"> > > > ___ > 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
Re: [Freesurfer] problem with mris_label2annot
does it work if you don't use --maxstatwinner ? On 05/13/2015 05:31 PM, Aaron Goldman wrote: > Hello, > > >From the standard "fsaverage" subject, I'm trying to map a series of > labels (?h.oasis.chubs.*) to a group of my own subjects. My end goal > is to create summary files equivalent to ?h.aparc.stats for each > subject. For sample commands, I've been looking at the "BA label" > section of a subject's recon-all.log > > For my test subject, I first ran mris_label2label on each of the seven > regions for each hemisphere, and then I visually confirmed that the > labels were generated correctly. Here's an example of those commands: > > mri_label2label --srcsubject fsaverage --srclabel > $FREESURFER_HOME/subjects/fsaverage/label/lh.oasis.chubs.ifc.label > --trgsubject $subj --trglabel > $SUBJECTS_DIR/$subj/label/lh.oasis.chubs.ifc.label --hemi lh > --regmethod surface > > However, I ran into trouble when I tried to combine the labels into an > annotation file. This is the command I'm using: > > cd $subj/label > mris_label2annot --s $subj --hemi $hemi --ctab > ~/colortable_oasis.chubs.txt --l lh.oasis.chubs.ifc.label --l > lh.oasis.chubs.ipc.label --l lh.oasis.chubs.ips.label --l > lh.oasis.chubs.lateraltemporal.label --l > lh.oasis.chubs.medialpfc.label --l lh.oasis.chubs.mtl.label --l > lh.oasis.chubs.retrosplenial.label --l lh.oasis.chubs.tp.label --a > oasis.chubs --maxstatwinner --noverbose > > And these are the contents of colortable_oasis.chubs.txt, which I > created by modifying /usr/local/freesurfer/average/colortable_BA.txt: > > 0 unknown 25 5 250 > 1 oasis.chubs.ifc 0 92 230 > 2 oasis.chubs.ipc 131 148 2550 > 3 oasis.chubs.ips 0 0 2550 > 4 oasis.chubs.lateraltemporal 255 102 510 > 5 oasis.chubs.medialpfc 196 255 200 > 6 oasis.chubs.mtl 255 51 2040 > 7 oasis.chubs.retrosplenial 1 38 1530 > 8 oasis.chubs.tp 153 0 380 > > The problem is, when I inspect the annotation file, I'm ending up with > the entire brain labeled "unknown". Any ideas what I'm doing wrong? > > Thanks, > > Aaron > > > ___ > 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] isxconcat-sess
Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] ROI Analysis
Hello Freesurfer experts, I ran an analysis using mri_glmfit and a manually drawn label of the parietal lobe that was mapped to every subject and a tablefile was used as the dependent measure. The output is a negative log 10 p-value. I was curious if I could possibly view that in freeview on an fsaverage lh.inflated surf file and would the sig.mgh file even show up with any hopefully uncorrected clusters within my ROI or is it too small of a significance value to be displayed? Thanks, Chris ___ 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] xhemi final iteration
Hi Doug, Thanks for your help. When I run the following command: images$ make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --fsgd laterality.fsgd --xhemi --lh ___ 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] isxconcat-sess
I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > Hi, >Does anyone know what has changed in isxconcat-sess command in > nmr-dev-env? Previously I could use it to average different sessions > of the same subject. But now I am getting this error: > > INFO: trgsubject is self, this will fail unless all sessions are the > same subject > ERROR: cannot find > /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz > > Regards > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > ___ > 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] xhemi final iteration
can you run it with --debug as the first option and send the terminal output? On 05/14/2015 05:35 PM, Derek James Dean wrote: > > Hi Doug, > > Thanks for your help. > > When I run the following command: > images$ make_average_subject --out myatlas.i3 --surf-reg > myatlas.i2.sphere.reg --fsgd laterality.fsgd --xhemi --lh > > > ___ > 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] xhemi final iteration
Here is the debug output. ~$ cd $SUBJECTS_DIR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] xhemi final iteration
there's nothing there (?) On 05/14/2015 06:13 PM, Derek James Dean wrote: > Here is the debug output. > > > > ~$ cd $SUBJECTS_DIR > > > ___ > 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] xhemi final iteration
Sorry about that, Outlook seems to be preventing me from sending the code in email. I have attached a text document of the output. output Description: output ___ 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] isxconcat-sess
Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve wrote: > I just made a fix. Can you try it out and let me know if it works? > > On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > > Hi, > >Does anyone know what has changed in isxconcat-sess command in > > nmr-dev-env? Previously I could use it to average different sessions > > of the same subject. But now I am getting this error: > > > > INFO: trgsubject is self, this will fail unless all sessions are the > > same subject > > ERROR: cannot find > > > /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz > > > > Regards > > -- > > Shahin Nasr > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > > > ___ > > 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 > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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.
