21 May
2019
21 May
'19
2:12 p.m.
I cannot replicate this. Can you look in the input labels and verify that they are not empty? Also, the "&" may be causing problems with the unix shell. Try using one that does not have an ampersand to see if it works.
On 5/21/19 4:31 AM, Michal Tanzer wrote:
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-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto: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-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@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." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <4f503934-d973-7563-2a14-235cb86012c6@mgh.harvard.edu <mailto:4f503934-d973-7563-2a14-235cb86012c6@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 <mailto: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." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] MP-RAGE protocol To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <e482d81c-774b-00ea-a70e-809139c87bb5@mgh.harvard.edu <mailto:e482d81c-774b-00ea-a70e-809139c87bb5@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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> > <mailto: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> > <mailto: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> <mailto: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> <mailto: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> <mailto: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 ------------------------------ Message: 3 Date: Mon, 20 May 2019 16:59:08 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] Question about recon-all.v6.hires To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <c6c9e090-4ae9-1307-aad4-ac0822b1eed3@mgh.harvard.edu <mailto:c6c9e090-4ae9-1307-aad4-ac0822b1eed3@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 <mailto: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" <ZNASIRIAVANAKI@mgh.harvard.edu <mailto:ZNASIRIAVANAKI@mgh.harvard.edu>> Subject: Re: [Freesurfer] mkanalysis-sess refeventdur To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com <mailto:DM6PR04MB44432A081ED580B5F392F5F199060@DM6PR04MB4443.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="us-ascii" Got it. Thank you very much for your reply Mona ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> Sent: Monday, May 20, 2019 12:52:39 PM To: freesurfer@nmr.mgh.harvard.edu <mailto: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 <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