Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

TrackVis question
by Alan Francis 24 May '19

24 May '19

External Email - Use Caution Hi Ruopeng - I used Diffusion Toolkit to recon DTI data that was preprocessed using FSL. This data is from 7T scanners. I used an Angle threshold of 50. I tried various gradients from 6 - 120, but the images I am getting on trackvis are weird. I have attached a screenshot. Can you please shed some light on this? Thank you, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

2 2

question on surface analysis
by Barletta, Valeria 24 May '19

24 May '19

Dear Freesurfer, I have a surface file containing values of a cortical myelination index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh) What I need to do is: - Masking the surface file with the lesion mask, to create a new lesion mask that contains the myelination index values from rh.MS075_CME.mgh; - Assess the percentage (or also the absolute number) of vertices that are under a certain threshold of myelination index values whithin the new lesion mask. What is the best way to do this? Thank you, Vale

2 4

XL defect in recon-all
by Barletta, Valeria 24 May '19

24 May '19

Dear Freesurfers, I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54, measuring over 20,000 voxels!! How do I check, and eventually fix, this defect? Thank you, Vale

2 3

Postdoctoral fellowships available in Toronto
by Rosanna Olsen 23 May '19

23 May '19

External Email - Use Caution The Rotman Research Institute at Baycrest (RRI) is seeking 9 outstanding postdoctoral fellows. A sub-set of the prospective fellows will be selected to be sponsored as the institutional candidates for a Banting Post-Doctoral Fellowship, and will work together with their prospective supervisors on the applications. [banting.fellowships-bourses.gc.ca <http://banting.fellowships-bourses.gc.ca/en/home-accueil.html>] The Rotman Research Institute (RRI) of Baycrest is a premier interdisciplinary, international centre for the study of human brain function. Our core research themes are: Cognitive Neuroscience, Aging and Brain Health, Alzheimer’s and Related Diseases, Computational Modeling and Neuroinformatics. Our research focuses on cognitive brain functions (including memory, executive function, attention, perception, and language), both in normal aging and in the presence of diseases and conditions that affect the brain, such as Alzheimer’s disease and other dementias, stroke, and traumatic brain injury. The Rotman Research Institute supports behavioral, neuropsychological, neuroimaging, and neurocomputational studies with state-of-the-art facilities, including eye-tracking, electroencephalography, and magnetoencephalography laboratories and a research-dedicated Siemens 3 Tesla MRI in-house at Baycrest. Rotman scientists who are currently recruiting post-doctoral fellows are: Jean Chen jchen(a)research.baycrest.org Brian Levine blevine(a)research.baycrest.org Randy McIntosh rmcintosh(a)research.baycrest.org Jed Meltzer jmeltzer(a)research.baycrest.org Morris Moscovitch momos(a)psych.utoronto.ca Rosanna Olsen rolsen(a)research.baycrest.org Jennifer Ryan jryan(a)research.baycrest.org Allison Sekuler vpr(a)research.baycrest.org and Eugenie Roudaia eroudaia(a)research.baycrest.org Stephen Strother sstrother(a)research.baycrest.org The postdoctoral fellows will conduct research on topics related to the areas of expertise of their prospective supervisors. In addition, fellowships at the RRI offer ample opportunities for collaborations both within the institute and with other researchers in Toronto. To find out more about recruiting scientists’ research areas, as well as a list of all scientists at the RRI, please follow individual links from here: https://www.baycrest.org/Baycrest/Research-Innovation/People/Researchers/Sc… Responsibilities and research opportunities may include but are not limited to: • Experimental design, data collection and analysis,manuscript preparation • Behavioural studies, including eyetracking • Structural neuroimaging with an emphasis on markers of learning-related changes • Multimodal functional neuroimaging, including fMRI, MEG, and/or EEG • Neurostimulation including tDCS, TMS • Data analysis using advanced, multivariate statistical tools applied to neuroimaging data Qualifications include but are not limited to: • Ph.D., M.D. or equivalent degree with an emphasis on neuropsychological theory • Experience in multivariate statistical techniques for data exploration, presentation, and analysis with advanced statistical software (e.g., R, MATLAB, Python) • Experience recruiting and testing research participants and patients • Experience with MRI, EEG, or MEG data collection and analysis The Banting Fellowships are open to Canadian citizens, Permanent Residents and Foreign Citizens. Starting dates are negotiable with the respective supervisors. To apply, please contact directly the scientist you wish to apply to, with a CV and cover letter, no later than *JUNE 10, 2019*. -- *Rosanna Olsen* Scientist, Rotman Research Institute *T* 416-785-2500, ext. 3509 rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen *Baycrest Health Sciences* <http://www.baycrest.org/?utm_source=Signature&utm_medium=Email&utm_campaign…> 3560 Bathurst Street, Toronto, ON, M6A 2E1 Baycrest.org <http://www.baycrest.org/?utm_source=Signature&utm_medium=Email&utm_campaign…> | Facebook <http://www.facebook.com/baycrestcentre> | Twitter <http://www.twitter.com/baycrest> | LinkedIn <https://www.linkedin.com/company/baycrest> | YouTube <https://www.youtube.com/user/TheBaycrestChannel> | Instagram <http://instagram.com/baycrest>

1 0

Hind's V1 Error for Freesurfer 6
by Lutz,Olivia (BIDMC - Psychiatry) 23 May '19

23 May '19

Dear Freesurfer group, We are interested in processing the Hind's V1 areas in addition to the Broadman areas. I am using a developmental verison of Freesurfer 6 from 1/18/2019 on Centos 6. I copied the V1_average into my $SUBJECTS_DIR folder and ran the following command on one subject (JS4501) as per the instructions the site https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps? >recon-all -s JS4501/ -label_v1 However, Freesurfer provides the following error: >ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-dev/utils/mrisurf_vals.c:4113 false ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-dev/utils/mrisurf_vals.c:4113 false /usr/local/freesurfer/bin/predict_v1.sh: line 123: 32339 Segmentation fault $cmd threshold_labelfile_at_0p8 /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.prob.label /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.predict.label thresholding the label...cat: /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.prob.label: No such file or directory done @#@FSTIME 2019:05:22:13:08:17 predict_v1.sh N 3 e 831.12 S 0.41 U 831.05 P 100% M 256512 F 0 R 316437 W 0 c 332 w 20 I 0 O 8976 L 3.12 3.00 3.13 @#@FSLOADPOST 2019:05:22:13:22:08 predict_v1.sh N 3 1.75 1.91 2.39 Started at Wed May 22 12:55:23 EDT 2019 Ended at Wed May 22 13:22:08 EDT 2019 #@#%# recon-all-run-time-hours 0.446 recon-all -s JS4501 finished without error at Wed May 22 13:22:08 EDT 2019 done As a result, the rh.v1.predict.label & lh.v1.predict.label are generated but there are no v1.prob.labels. Is there anything I need to adjust to generate the Hind's V1 maps? Thanks! Olivia ________________________________ 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.

1 0

Re: [Freesurfer] recon-all exited ERRORS
by jennifer sorinas 23 May '19

23 May '19

External Email - Use Caution Dear Qiannan, I’m having the same problems, recon-all -all command is not working. FreeSurfer Developers help please! 😊 Best, Jennifer Enviado desde Correo<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

3 4

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

1 0

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

2 2

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

3 2

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 >

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer