Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Skull-stripping issue: both over and under skull-stripping estimations
by Amy Paulson 22 May '19

22 May '19

External Email - Use Caution Hello FreeSurfer Developers, I have been attempting to compare FSL lesion-filled patients to their non lesion-filled counterparts. However, with this particular subject the skull-stripping has both over estimated and under estimated areas within the brain. I’m attaching a few pictures to show what I’m referring to. I have tried using both FSL (bet), as well as, performing watershed manipulation as described in the recon-all step -skullstrip, but both haven’t been able to fix the problem. I was wondering if you guys would know the best approach to solving this problem? I have tried to search for similar skull-stripping discussions, but did not find any other possible solutions. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS Mojave v10.14.5 recon-all.log: see attached Amy Paulson Research Assistant University of Minnesota Department of Pediatrics | 717 Delaware Minneapolis, MN 55414 Phone: 952-288-5110

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FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy
by Verma, Gaurav 22 May '19

22 May '19

External Email - Use Caution Dear FreeSurfer Community, In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 isotropic) versions of the same data we have received conflicting volume data in our aseg.stats file. Below is the relevant excerpt from those files. High-resolution (0.7 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 3264609.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1330806.023066, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 60940.000000, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 230160.306401, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 228696.462181, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 458856.768582, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 158718.858711, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 161112.395773, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 319831.254484, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 149905.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 941078.768582, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 970862.023066, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 909922.023066, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 2790169.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.000000, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 2.065785, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 2.943701, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 46, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 70, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 116, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1580323.941985, mm^3 Low resolution (1.0 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1132377.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1106786.650039, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 21069.000000, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 226998.297110, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 225122.819041, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 452121.116151, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 228780.783147, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235221.750741, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 464002.533888, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 51537.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 619358.116151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 990616.650039, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 969547.650039, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 968494.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.000000, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.714626, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.993586, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 30, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 27, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 57, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1584573.435767, mm^3 Some of the measures, like eTIV, lhCortexVol and rhCortexVol are in good agreement. Others, like BrainSegVol, SubCortGrayVol and VentricleChoroidVol seem to be off by a factor of 0.7^3 = 0.343. Still others like TotalGrayVol and CerebralWhiteMatterVol seem to disagree in ways that are not obvious. The data are not shown but the subcortical gray matter volumes for specific areas seem to be in good agreement. The relevant function calls that were used to generate these files are: recon-all -s <subj_id > <input_T1_file> -all -openmp 4 And the command I ran for the high-res (sub-mm) segmentation is recon-all -s <subj_id> <input_T1_file> -all -cm -expert expert.txt -openmp 4 And the content of expert.txt is just one line: mris_inflate -n 15 I wanted to ask if anyone could identify the source of these discrepancies, or how to resolve them. In particular I'm interested in how to resolve discrepancies in volumes which don't seem to be off by a scaling factor like TotalGrayVol. Thank you very much! Gaurav Verma

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number of vertices
by Sam W. 21 May '19

21 May '19

External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam

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Re: [Freesurfer] mris_label2annot empty Annot
by Michal Tanzer 21 May '19

21 May '19

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(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)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(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] mkanalysis-sess refeventdur > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <4f503934-d973-7563-2a14-235cb86012c6(a)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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] MP-RAGE protocol > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <e482d81c-774b-00ea-a70e-809139c87bb5(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: > Freesurfer(a)nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about recon-all.v6.hires > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <c6c9e090-4ae9-1307-aad4-ac0822b1eed3(a)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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] mkanalysis-sess refeventdur > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > DM6PR04MB44432A081ED580B5F392F5F199060(a)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(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > Sent: Monday, May 20, 2019 12:52:39 PM > To: freesurfer(a)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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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problem with mri_surfcluster
by Barletta, Valeria 21 May '19

21 May '19

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

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Mri glmfit sim error
by Amrita Bedi 21 May '19

21 May '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Tuesday, May 21, 2019 Subject: To: "amibedi273(a)gmail.com" <amibedi273(a)gmail.com> Hi Freesurfer developers, While running the mri glmfit sim command for a smoothing of 30 FWHM, I got the following error- Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.BINGE15.g2v1.30B.mgh --fsgd BINGE15.g2v1.txt dods --C BINGE.g2v1.group-x-LDH_age.mtx --surf fsaverage lh --cortex --glmdir lh.BINGE15_g2v1.group-x-LDH_age.30B.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 53.156463 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ cortex/fwhm53/abs/th13/mc-z.csd I researched on the Freesurfer wiki page and found Dr Greve answered a similar question saying-"When running mri_glmfit-sim, add --cache-dir /path/to/mult-comp-cor" but I dont understand. What is this path? Thank You! Best, Amrita

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Postdoctoral fellowship in cognitive neuroscience at UCSF
by Maria Luisa Mandelli 21 May '19

21 May '19

External Email - Use Caution The ALBA Language Neurobiology laboratory or the UCSF Memory and Aging Center has an open postdoctoral position in cognitive neuroscience. Directed by Dr. Maria Luisa Gorno Tempini, the ALBA lab conducts cutting-edge research on the cognitive and neural correlates of language and related cognitive functions across the life span. In particular, neurodegenerative as well as neurodevelopmental disorders, including frontotemporal dementia, primary progressive aphasia, and dyslexia, are used as clinical models. The postdoctoral fellow will contribute to ongoing experiments and pursue self-directed projects within the lab’s area of investigation. Working closely with the current members of the team, he/she will contribute to our empirical efforts to further our understanding of the neurobiology of language. The ideal candidate will have expertise in either cognitive neuroscience or neuroimaging (in particular understanding of, and experience with, fMRI data analysis). Excellent English (oral and written) and good communication skills are necessary. Strong computational and programming skills are preferred. Appropriate areas of doctoral training include, but are not limited to, cognitive neuroscience, psychology, and computer science. The successful candidate would join the multidisciplinary team of world-class neurologists, neuropsychologists, speech-language pathologists, engineers, and cognitive scientists working at the UCSF - Memory and Aging Center, the largest cognitive and behavioral neurology center in the United States. Cognitive neuroscience research will integrate our rich, multidisciplinary datasets to study the cognitive, clinical, anatomical, and neuropathological correlates of disease. To apply, please send a cover letter, a CV, and 3 names of potential references to elizabeth.weis(a)ucsf.edu Informal inquiries are most welcome. -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420 -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420

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Reminder: OHBM 2019 Brain-Art Competition is open for submissions! {Disarmed}
by Maria Luisa Mandelli 21 May '19

21 May '19

External Email - Use Caution The OHBM Brain-Art SIG <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanbrainmapping.…> 2019 Brain-Art Competition is open for submissions! This competition aims at fostering the dialog between art and science. We believe that the exchange of ideas and tools between these two disciplines encourages the development of novel approaches to scientific data visualization, and promotes the exploration of different perspectives on human brain structures and functions. Everyone is encouraged to submit original work(s)! There is no limit to the number of submissions per participant, and both team and single-person entries are welcome. All submitted pieces will be exhibited during the OHBM 2019 Annual Meeting in Rome <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanbrainmapping.…>. This year submissions will be accepted to the following categories *1. Erato: **2D *i.e., digital images such as drawings, photos, paintings. *2. Clio: **3D *i.e., sculptures and installations. Note that any 3D submission should be entered as a photo then shipped/brought to Rome. Please reach out to us should this be impossible. *3. Calliope: **1D *i.e., short texts (one-page maximum) with or without illustrations such as short fiction or poetry. *4. Terpsichore: real-time performance *i.e., any performative act (e.g. singing, dancing, live sketching, etc…). Please note that a one-page max description should be entered at time of submission, then the act should be performed during the conference. *5. Melpomene*: *failed attempt / bug / artifact* Key information: - Submission Deadline: *Friday, May 31st, 2019, midnight eastern time* - Award Notificaiton: Monday, June 10th, 2019 - Submission portal: https://www.neurobureau.org/brainart/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.neurobureau.org_br…> -- Maria Luisa Mandelli, PhD Associate Professional Researcher UCSF Department of Neurology 675 Nelson Rising Lane Mission Bay Campus San Francisco, CA 94158 phone (415) 353-9420

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Fixing of Morphometry Stats and Global Measure of Volume: Longitudinal analysis
by Diana Tordesillas-Gutiérrez 21 May '19

21 May '19

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 -- -------------------------------------------------------- Diana Tordesillas Gutiérrez, PhD Neuroimaging Unit IDIVAL IDIVAL Building Avda. Cardenal Herrera Oria s/n 39011 Santander Spain Tel. +34 942202677 diana.tordesillas(a)idival.org diana.tordesillas(a)gmail.com CIBERSAM G26 ----------------------------------------------------------

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Moving data files
by Mingzhu Hou 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer team / community, This is a very basic and general question. I am currently setting up for a team in our lab to use the Freesurfer automated pipeline for thickness / volumetric measures on hundreds of adult brains. As there will be around 7 people working on these data (each working on different subsets of the data), I am planning to set up different working directories for each researcher’s subset of subjects to avoid possible confusion / overwriting etc. for the initial recon, manual editing and re-recon. Once happy with the re-recon, I plan for all individual S folders to be moved to one general data folder for further analysis. I am just concerned that moving S folders between initial individual processing/analysis and further group analyses will cause problems if, say, there is directory information embedded within any of the files during initial processing. Does anyone know if moving these files in this way might cause problems at some point, or is it advised to keep individual S folders in the same directory throughout? Thanks in advance for your help. Best, Mingzhu

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Freesurfer May 2019