External Email - Use Caution Hi Thank you for your response, here is the terminal output: It does create a new annot, but it's empty.
bw Michal cwd /Applications/freesurfer/subjects/Alldata6V/bert cmdline mris_label2annot --s bert --h lh --ctab label/aparc.annot.a2009s.ctab --a myaprac11 --l dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug subject bert hemi lh SUBJECTS_DIR /Applications/freesurfer/subjects/Alldata6V ColorTable label/aparc.annot.a2009s.ctab AnnotName myaprac11 nlables 2 LabelThresh 0 0.000000 Loading /Applications/freesurfer/subjects/Alldata6V/bert/surf/lh.orig 1 -1 NOT_FOUND 2 -1 NOT_FOUND Mapping unhit to unknown Found 131576 unhit vertices On Mon, 20 May 2019 at 20:11, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mkanalysis-sess refeventdur (Greve, Douglas N.,Ph.D.) > 2. Re: MP-RAGE protocol (Greve, Douglas N.,Ph.D.) > 3. Re: Question about recon-all.v6.hires (Greve, Douglas N.,Ph.D.) > 4. Re: mkanalysis-sess refeventdur (Nasiriavanaki, Zahra) > 5. problem with mri_surfcluster (Barletta, Valeria) > 6. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.) > 7. Re: mris_label2annot empty Annot (Greve, Douglas N.,Ph.D.) > 8. Re: problem with mri_surfcluster (Barletta, Valeria) > 9. Re: Fixing of Morphometry Stats and Global Measure of Volume: > Longitudinal analysis (Greve, Douglas N.,Ph.D.) > 10. Re: problem with mri_surfcluster (Greve, Douglas N.,Ph.D.) > 11. Re: problem with mri_surfcluster (Barletta, Valeria) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 May 2019 16:52:39 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] mkanalysis-sess refeventdur > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <4f503934-d973-7563-2a14-235cb8601...@mgh.harvard.edu> > Content-Type: text/plain; charset="Windows-1252" > > No, you'll need to change your paradigm file to have two distinct 8 sec > events rather than one 16 sec event. > > On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote: > > > > Hi Freesurfer experts > > > > > > I am?making an analysis in Freesurfer version 6 and?I have a question > > about the "refeventdur" in mkanalysis-sess command. > > > > My stimulus duration is 16 seconds, but for a specific analysis, I > > only want to include half of the stimulus duration (ex:?the?first 8 > > seconds only OR the?last 8 seconds only). > > > > I was wondering if I can do this, by setting the "refeventdur" to 8 > > seconds.? Will that work? and if it does, is it including the first 8 > > seconds or the last 8 seconds? > > > > > > Thanks > > > > Mona > > > > > > > > *Zahra?(Mona) Nasiriavanaki* > > > > Postdoctoral Research Fellow > > > > Martinos Center for Biomedical Imaging > > > > Massachusetts General Hospital > > > > 149 13th Street, 149-2615 > > > > Charlestown, MA, USA, 02129 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 2 > Date: Mon, 20 May 2019 16:55:39 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] MP-RAGE protocol > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e482d81c-774b-00ea-a70e-809139c87...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Your attachment says that none of the commands could be found. Make sure > you set up your environment correctly > > On 5/20/19 4:53 AM, mustafa amin wrote: > > > > ????????External Email - Use Caution > > > > Hi Bruce, > > > > Thank you for your swift response as always, may I know how to convert > > the more than 100 DICOM files to mgz or nifti? I noticed that the > > command is for 1 file/image, please correct me if I am wrong. The > > MP-RAGE file that I sent you is more than 50 images. > > > > I tried to follow your instruction however it did not work smoothly. > > The diacom files couldn't be converted to mgz. I have attached the > > command that still did not work when I used them in this email. Please > > have a look and share some thoughts. Thank you for your kind attention > > and cooperation. > > > > > > Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> menulis: > > > > > > Hi Mustafa > > > > 1. Your mprage ran through recon-all fine and the results look good. The > > saggital field of view is tight, so make sure that they don't crop > > brain in > > that direction. > > > > 2. Your recon-all command line is incorrect. You should point the > > SUBJECTS_DIR environment variable to whereever you want to store all of > > your FreeSurfer-processed data, then use the -i switch to path to the > > input > > volume. You can also specify SUBJECTS_DIR on the command line. So in your > > case something like: > > > > > > recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 > > -sd \ > > ??? ? /path/to/my/subjecs -all > > > > should do the trick. There is also no need to convert to nifti first > > > > cheers > > Bruce > > > > > > On Fri, > > 17 May 2019, mustafa amin wrote: > > > > > > > > ????????External Email - Use Caution > > > > > > > > Hi Bruce, > > > > > > Herewith I attach within the email the command that didn't work when > > I wanted to reconall. Please > > > have a look. What about the previous dicom that I have sent to you? > > Please share some thoughts.Thank > > > you very much. > > > > > > Yours faithfully, > > > > > > Mustafa > > > > > > > > > Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> > menulis: > > > > > > > > > Hi Mustafa > > > > > > can you give us some detials? What didn't work? Can you send us the > full > > > command line, screen output and recon-all.log? > > > > > > cheers > > > Bruce > > > > > > > > > On Thu, 16 May 2019, mustafa amin wrote: > > > > > > > > > > > ????????External Email - Use Caution > > > > > > > > Hi Douglas, > > > > > > > > I tried to follow the instruction to recon-all the data however it > > didn't work. Please give > > > > some thoughts. Thank you in advance. > > > > > > > > Yours faithfully, > > > > > > > > Mustafa > > > > > > > > Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > > > > menulis: > > > > > > > > > > > > Hi Mustafa, why not just run recon-all on the data you have and see > > > > whether it looks ok? > > > > > > > > On 4/15/19 7:06 AM, mustafa amin wrote: > > > > >? ? ? ? ? External Email - Use Caution > > > > > > > > > > Hi Bruce, > > > > > > > > > > I?ve talked to the MRI operator and she told me that the best > > thing to do the MP-RAGE > > > > protocol is doing the T1 weighted 3D gradient echo with SENSE, she > > can?t set the TE, TR, TI > > > > just like the ADNI protocol asked, though. She can set the > > thickness to 1 mm. Is this set > > > > up okay? > > > > > > > > > > I have the DIACOM files of some subjects with the set up above. > > Can I send them to you to > > > > look at them? > > > > > > > > > >? I am terribly sorry for keep asking this basic question due to > > we never had experience > > > > doing it in Indonesia. > > > > > > > > > > Many thanks! > > > > > > > > > > > > > > > Mustafa M. Amin > > > > > Consultant Psychiatrist in Biological Psychiatry > > > > > Department of Psychiatry > > > > > Faculty of Medicine > > > > > Universitas Sumatera Utara > > > > > > > > > >> On 2 Apr 2019, at 20.49, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > >> > > > > >> Hi Mustafa > > > > >> > > > > >> MRI is an amazingly versatile technology that can be messed up > > in an > > > > >> astonishing number of ways. By far the best thing to do would > > be to acquire > > > > >> a dataset and run it through recon-all and see if the results look > > > > >> accurate. If you have permission to do so, you are welcome to > > acquire one > > > > >> and send it to us to try out instead. > > > > >> > > > > >> cheers > > > > >> Bruce > > > > >> > > > > >> On Tue, 2 Apr 2019, mustafa amin > > > > >> wrote: > > > > >> > > > > >>>? ? ? ? External Email - Use Caution > > > > >>> > > > > >>> Dear Freesurfer experts, > > > > >>> > > > > >>> I need advice, the MRI operator need to confirm whether she > > had done the > > > > >>> right protocol of MP-RAGE. I have attached the picture that > > has been > > > > >>> taken by her. Please share some thoughts. Thank you in advance. > > > > >>> > > > > >>> > > > > >> _______________________________________________ > > > > >> Freesurfer mailing list > > > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 3 > Date: Mon, 20 May 2019 16:59:08 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about recon-all.v6.hires > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <c6c9e090-4ae9-1307-aad4-ac0822b1e...@mgh.harvard.edu> > Content-Type: text/plain; charset="Windows-1252" > > They should be there. Can you send recon-all.log and conf2hires.log files? > > On 5/20/19 9:59 AM, Bruce Fischl wrote: > > Hi Victor > > > > the lh.white.{KH} are generated from the lh.white file, so I don't > > think it can have skipped creating it. Was it deleted? Can you double > > check? > > > > Bruce > > On Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > > >> > >> Hi all, > >> > >> > >> I am running 7T scans through FS6, and I have been recommended to > >> install the tools > >> in? > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ > >> . So I ran the new > >> recon-all.v6.hires, specifically with the command "recon-all.hires.v6 > >> -s subj -conf2hires -all" > >> > >> > >> For the most part, it ran, but I while QCing, it couldn't seem to > >> load the surfs files. Recon-all > >> seemed to have generated files called ?h.white.H and ?h.white.K, but > >> apparently skipped the steps > >> for ?h.white? I don't think I can load the surfs files without it, > >> and I don't?know if this is > >> intentional. > >> > >> > >> Victor Zeng > >> Beth Israel Deaconess Medical Center > >> Keshavan Lab > >> -- > >> > >> > ____________________________________________________________________________________________________ > > >> > >> > >> This message is intended for the use of the person(s) to whom it may > >> be addressed. It may contain > >> information that is privileged, confidential, or otherwise protected > >> from disclosure under > >> applicable law. If you are not the intended recipient, any > >> dissemination, distribution, copying, or > >> use of this information is prohibited. If you have received this > >> message in error, please > >> permanently delete it and immediately notify the sender. Thank you. > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 4 > Date: Mon, 20 May 2019 18:08:34 +0000 > From: "Nasiriavanaki, Zahra" <znasiriavan...@mgh.harvard.edu> > Subject: Re: [Freesurfer] mkanalysis-sess refeventdur > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > dm6pr04mb44432a081ed580b5f392f5f199...@dm6pr04mb4443.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > Got it. > > Thank you very much for your reply > > > Mona > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > Sent: Monday, May 20, 2019 12:52:39 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mkanalysis-sess refeventdur > > No, you'll need to change your paradigm file to have two distinct 8 sec > events rather than one 16 sec event. > > On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote: > > > > Hi Freesurfer experts > > > > > > I am making an analysis in Freesurfer version 6 and I have a question > > about the "refeventdur" in mkanalysis-sess command. > > > > My stimulus duration is 16 seconds, but for a specific analysis, I > > only want to include half of the stimulus duration (ex: the first 8 > > seconds only OR the last 8 seconds only). > > > > I was wondering if I can do this, by setting the "refeventdur" to 8 > > seconds. Will that work? and if it does, is it including the first 8 > > seconds or the last 8 seconds? > > > > > > Thanks > > > > Mona > > > > > > > > *Zahra (Mona) Nasiriavanaki* > > > > Postdoctoral Research Fellow > > > > Martinos Center for Biomedical Imaging > > > > Massachusetts General Hospital > > > > 149 13th Street, 149-2615 > > > > Charlestown, MA, USA, 02129 > > > > > > > > > > _______________________________________________ > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190520/b5ab9d98/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 20 May 2019 18:40:25 +0000 > From: "Barletta, Valeria" <vbarle...@mgh.harvard.edu> > Subject: [Freesurfer] problem with mri_surfcluster > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > bn7pr04mb5185fb256479b0e8af6171f1f9...@bn7pr04mb5185.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Freesurfers, > > I am trying to obtain clusters of vertices whit a certain value over a > threshold inside a lesion mask projected to the surface, with the command: > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos --minarea > 0.01 --sum summary.txt > > But I obtain this result saying there are no vertices in my mask. > > thsign = pos, id = 1 > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > hemi = lh > srcid = > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > srcsubjid = MS075_R01_07_R1year > srcsurf = lh.pial > srcframe = 0 > thsign = pos > thmin = 1 > thmax = 49.9581 > fdr = -1 > minarea = 0.01 > xfmfile = talairach.xfm > nth = -1 > sumfile = > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > subjectsdir = > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > FixMNI = 1 > Found 0 vertices in mask > > > Can you help me figure out why? > > Thanks, > Vale > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190520/348ca2ec/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 20 May 2019 18:46:54 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] problem with mri_surfcluster > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <6a91d804-b0e6-bed2-dd04-24cb42a02...@mgh.harvard.edu> > Content-Type: text/plain; charset="Windows-1252" > > How did you choose thresholds of 1 and 49.95? In general, you don't need > to set --thmax. If you input is a binary mask, then you should set > --thmin to somethiing below 1 (eg, 0.5) > > On 5/20/19 2:40 PM, Barletta, Valeria wrote: > > > > Dear Freesurfers, > > > > I am trying to obtain clusters of vertices whit a certain value?over a > > threshold inside a lesion mask projected to the surface,?with the > command: > > > > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos > > --minarea 0.01 --sum summary.txt > > > > But I obtain this result saying there are no vertices in my mask. > > > > thsign = pos, id = 1 > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > > hemi? ? ? ? ? ?= lh > > srcid? ? ? ? ? = > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > > > > > srcsubjid? ? ? = MS075_R01_07_R1year > > srcsurf? ? ? ? = lh.pial > > srcframe? ? ? ?= 0 > > thsign? ? ? ? ?= pos > > thmin? ? ? ? ? = 1 > > thmax? ? ? ? ? = 49.9581 > > fdr? ? ? ? ? ? = -1 > > minarea? ? ? ? = 0.01 > > xfmfile? ? ? ? = talairach.xfm > > nth? ? ? ? ?= -1 > > sumfile? = > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > > subjectsdir? ? = > > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > > FixMNI = 1 > > Found 0 vertices in mask > > > > > > Can you help me figure out why? > > > > Thanks, > > Vale > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 7 > Date: Mon, 20 May 2019 18:50:25 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] mris_label2annot empty Annot > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e13d70d6-4856-a7fb-935d-31104f073...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Can you send the terminal output? > > On 5/20/19 8:51 AM, Michal Tanzer wrote: > > > > ????????External Email - Use Caution > > > > Dear Freesurfer experts, > > I am having some difficulties in creating annot file for specific ROIs > > using the 2009atlas. When I am using this command, it saves the annot > > but I am getting empty files. Using the same command with the > > aparc.annot file and different ROIs seems fine, so I am not sure what > > is the problem. > > > > mris_label2annot --s fsaverage --h lh --ctab > > label/aparc.annot.a2009s.ctab --a myaprac--l > > dir/lh.G_insular_short.label --l dir/lh.G_Ins_lg&S_cent_ins.label --debug > > > > Thank you for your help, > > > > Kind regards, > > Michal > > -- > > Michal Tanzer, PhD > > > > Postdoctoral fellow; Clinical Psychologist. > > Research Department of Clinical, Educational and Health Psychology, > > University College London, > > United Kingdom > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 8 > Date: Mon, 20 May 2019 18:51:09 +0000 > From: "Barletta, Valeria" <vbarle...@mgh.harvard.edu> > Subject: Re: [Freesurfer] problem with mri_surfcluster > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > bn7pr04mb518570c9b3afa4c4af223b9df9...@bn7pr04mb5185.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > I want to extract clusters within the cortical lesion mask in which the > vertex values are below 49.95 > > The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh > > > Thanks, > > Vale > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > Sent: Monday, May 20, 2019 2:46:54 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] problem with mri_surfcluster > > How did you choose thresholds of 1 and 49.95? In general, you don't need > to set --thmax. If you input is a binary mask, then you should set > --thmin to somethiing below 1 (eg, 0.5) > > On 5/20/19 2:40 PM, Barletta, Valeria wrote: > > > > Dear Freesurfers, > > > > I am trying to obtain clusters of vertices whit a certain value over a > > threshold inside a lesion mask projected to the surface, with the > command: > > > > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos > > --minarea 0.01 --sum summary.txt > > > > But I obtain this result saying there are no vertices in my mask. > > > > thsign = pos, id = 1 > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > > hemi = lh > > srcid = > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > > > > srcsubjid = MS075_R01_07_R1year > > srcsurf = lh.pial > > srcframe = 0 > > thsign = pos > > thmin = 1 > > thmax = 49.9581 > > fdr = -1 > > minarea = 0.01 > > xfmfile = talairach.xfm > > nth = -1 > > sumfile = > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > > subjectsdir = > > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > > FixMNI = 1 > > Found 0 vertices in mask > > > > > > Can you help me figure out why? > > > > Thanks, > > Vale > > > > > > > > > > _______________________________________________ > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190520/ff6710f8/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Mon, 20 May 2019 18:54:36 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Fixing of Morphometry Stats and Global > Measure of Volume: Longitudinal analysis > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <67db3b4a-4ea4-2640-f769-7600311da...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > You will not need to run the entire stream again. Did you run it in > high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm, > 252^3), then you do not need to do anything. Otherwise, you will need to > re-run only part of it using the patch and running > > recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 > -wmparc -balabels > > I think this should work fine on longitudinal data, but run it on one to > make sure > > See https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed for > more info > > > > On 5/20/19 4:06 AM, Diana Tordesillas-Guti?rrez wrote: > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I have a question about the bug in FreeSurfer v.6? in the global metrics > > computation: > > > > I have run my data through the longitudinal pipeline. I would like to > > know if my analysis have been affected (3T, voxel size 0.94) and I have > > to rerun the whole analysis in case they have. > > > > Thank you! > > > > Diana > > > > > > > ------------------------------ > > Message: 10 > Date: Mon, 20 May 2019 18:56:38 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] problem with mri_surfcluster > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8a6b12bc-9a30-ae81-aa68-3c69ebf24...@mgh.harvard.edu> > Content-Type: text/plain; charset="Windows-1252" > > When you look at the overlay in freeview and set the min thresh to 1, do > you see blobs? > > On 5/20/19 2:51 PM, Barletta, Valeria wrote: > > > > I want to extract clusters within the cortical lesion mask?in which > > the vertex values are below 49.95 > > > > The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh > > > > > > Thanks, > > > > Vale > > > > ------------------------------------------------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > > N.,Ph.D. <dgr...@mgh.harvard.edu> > > *Sent:* Monday, May 20, 2019 2:46:54 PM > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] problem with mri_surfcluster > > How did you choose thresholds of 1 and 49.95? In general, you don't need > > to set --thmax. If you input is a binary mask, then you should set > > --thmin to somethiing below 1 (eg, 0.5) > > > > On 5/20/19 2:40 PM, Barletta, Valeria wrote: > > > > > > Dear Freesurfers, > > > > > > I am trying to obtain clusters of vertices whit a certain value?over a > > > threshold inside a lesion mask projected to the surface,?with the > > command: > > > > > > > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > > > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > > > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos > > > --minarea 0.01 --sum summary.txt > > > > > > But I obtain this result saying there are no vertices in my mask. > > > > > > thsign = pos, id = 1 > > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve > > Exp $ > > > hemi? ? ? ? ? ?= lh > > > srcid? ? ? ? ? = > > > > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > > > > > > srcsubjid? ? ? = MS075_R01_07_R1year > > > srcsurf? ? ? ? = lh.pial > > > srcframe? ? ? ?= 0 > > > thsign? ? ? ? ?= pos > > > thmin? ? ? ? ? = 1 > > > thmax? ? ? ? ? = 49.9581 > > > fdr? ? ? ? ? ? = -1 > > > minarea? ? ? ? = 0.01 > > > xfmfile? ? ? ? = talairach.xfm > > > nth? ? ? ? ?= -1 > > > sumfile? = > > > > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > > > subjectsdir? ? = > > > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > > > FixMNI = 1 > > > Found 0 vertices in mask > > > > > > > > > Can you help me figure out why? > > > > > > Thanks, > > > Vale > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 11 > Date: Mon, 20 May 2019 19:09:43 +0000 > From: "Barletta, Valeria" <vbarle...@mgh.harvard.edu> > Subject: Re: [Freesurfer] problem with mri_surfcluster > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > bn7pr04mb518533e1145813e9cd09b971f9...@bn7pr04mb5185.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > This is what I see if I set min 1 max 49 on the overlay (the > subjectspace.mgh file in the command) > > > > [cid:219fb126-a40e-4f06-9849-aac62b6aee0f] > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > Sent: Monday, May 20, 2019 2:56:38 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] problem with mri_surfcluster > > When you look at the overlay in freeview and set the min thresh to 1, do > you see blobs? > > On 5/20/19 2:51 PM, Barletta, Valeria wrote: > > > > I want to extract clusters within the cortical lesion mask in which > > the vertex values are below 49.95 > > > > The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh > > > > > > Thanks, > > > > Vale > > > > ------------------------------------------------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > > N.,Ph.D. <dgr...@mgh.harvard.edu> > > *Sent:* Monday, May 20, 2019 2:46:54 PM > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] problem with mri_surfcluster > > How did you choose thresholds of 1 and 49.95? In general, you don't need > > to set --thmax. If you input is a binary mask, then you should set > > --thmin to somethiing below 1 (eg, 0.5) > > > > On 5/20/19 2:40 PM, Barletta, Valeria wrote: > > > > > > Dear Freesurfers, > > > > > > I am trying to obtain clusters of vertices whit a certain value over a > > > threshold inside a lesion mask projected to the surface, with the > > command: > > > > > > > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > > > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > > > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos > > > --minarea 0.01 --sum summary.txt > > > > > > But I obtain this result saying there are no vertices in my mask. > > > > > > thsign = pos, id = 1 > > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve > > Exp $ > > > hemi = lh > > > srcid = > > > > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > > > > > > srcsubjid = MS075_R01_07_R1year > > > srcsurf = lh.pial > > > srcframe = 0 > > > thsign = pos > > > thmin = 1 > > > thmax = 49.9581 > > > fdr = -1 > > > minarea = 0.01 > > > xfmfile = talairach.xfm > > > nth = -1 > > > sumfile = > > > > > > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > > > subjectsdir = > > > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > > > FixMNI = 1 > > > Found 0 vertices in mask > > > > > > > > > Can you help me figure out why? > > > > > > Thanks, > > > Vale > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190520/74c56720/attachment.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screenshot at 2019-05-20 15-06-17.png > Type: image/png > Size: 509917 bytes > Desc: Screenshot at 2019-05-20 15-06-17.png > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190520/74c56720/attachment.png > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 183, Issue 27 > ******************************************* > -- Michal Tanzer, PhD Postdoctoral fellow; Clinical Psychologist. Research Department of Clinical, Educational and Health Psychology, University College London, United Kingdom
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